An entry in former Labour MP Chris Mullin's diary for 6 August 1999 describes one of his first days as a new minister. Two men visited him in his office to talk about security. He was one of five ministers in the Department of the Environment, Transport and the Regions whose responsibilities, in his case water and aviation, entitled them to see "STRAP 2 (Top Secret)" information.

Mullin reports the details of his conversation with the two men, one of whom he dubbed the Undertaker. He writes: "The Undertaker said, 'Some of the people we have to negotiate with are pretty uncivilised.' He added, 'Mind, we also deal with some very civilised people – and we spy on them, too.' The only people we don't spy on are the Americans, the New Zealanders, Australians and Canadians, who are all part of a little club that has agreed to share the products of their bugging, burglary and bribery."

It's now more than three months since the Guardian began publishing stories about the hidden extent of the US and UK governments' surveillance of their peoples. These stories have been based on tens of thousands of secret documents disclosed by the National Security Agency whistleblower Edward Snowden. We now know, because of him, quite a lot more about the two senior members of the "little club" of five, which includes the UK and is known as the "Five Eyes". These documents have revealed the scale and nature of the mass surveillance carried out through the NSA and the UK's Government Communications Headquarters (GCHQ).

It is a complex and evolving story that has led to Snowden, currently receiving temporary asylum in Russia, being charged under the 1917 Espionage Act in the US; it has also led to a criminal investigation into the disclosures being mounted in the UK.

The public learned about the UK investigation from a high court hearing in which Home Office and Metropolitan police lawyers were fighting for the right to continue to examine material seized from David Miranda. He is the partner of Glenn Greenwald, the Guardian journalist who brought the Snowden material to the paper and who has been at the heart of its coverage.

Miranda was on his way from Berlin – the home of film-maker Laura Poitras, his collaborator in the disclosures – to Brazil, where he and Greenwald live, when he was detained under an anti-terrorism law on 18 August. A computer and other equipment he was carrying were seized during his detention, which lasted nine hours.

The Snowden disclosures have been a major story for the Guardian and have provoked fierce debate in the US and many parts of the world. I would have expected to have written about it before for an Open Door column, but have waited for a number of reasons. First, it is a guiding principle that most such columns are based on readers' complaints and queries.

More than 300 articles have been published since the first, on 6 June 2013, which revealed that a top-secret court had ordered a US telephone company, Verizon, to hand over data on millions of calls. However, since then, the readers' editor's office has received only 108 emails in relation to the series, of which just 13 were critical. Of the 13, only two specifically criticised the Guardian for publishing the disclosures, which is unusual for such a high-profile story.

Of the rest, 48 were supportive of the Guardian's reporting, 27 offered further information or further case studies, and seven wanted to know how they could help Snowden, with some of them offering money, advice on visas, or even places to stay. A further 13 wanted to know more about what this kind of surveillance means for them personally.

Below the line there are thousands of comments but outright criticism of the Guardian for publishing is relatively rare. I asked the Guardian's moderators, who monitor all the comments, what their impressions are of the balance of views. One, in a fair reflection of the general view among his colleagues, said the commenters had "angrily debated the issues, but very few took any issue with us revealing them".

The second reason is that the readers' editor is given a chance not afforded to most journalists – time to step back and wait for the dust to settle before discussing whether the Guardian and its staff did the right or the wrong thing. There is not much sign of the dust settling just yet. The stories based on the documents keep coming, not just from the Guardian but from news organisations around the world.

First there was the Guardian and the Washington Post. Now, the Guardian, the New York Times and the investigative journalism website ProPublica are co-operating in the publication of the latest tranche of stories. In addition Der Spiegel, TV Globo in Brazil and others are all producing stories based on the Snowden material.

So, this column is a snapshot of the significant issues that have emerged from readers' questions and concerns.

First I spoke to Greenwald about the arguments, which come more often from rival newspapers and the intelligence agencies, that it was wrong to publish in the first place.

He said: "There are two strains of criticism about what the Guardian is doing. i) That we are endangering national security. ii) We are actually publishing too little, publishing too slowly, which I think is a more interesting critique.

"We have been extremely careful and cautious the whole time, probably careful to a fault. We have been determined not to unilaterally destroy programmes or put people in danger. Snowden was adamant that we engage in this very careful process. If we didn't it could render the debate ineffective. If anything, people have been concerned that we have been too much of a gatekeeper.

"I think you have to remember that you can always publish something that is unpublished but you can't unpublish something once it's published."

Concern that the Guardian is being too careful in its reporting is widely expressed online. One largely supportive reader from the US technical community wrote complaining to Alan Rusbridger, the Guardian's editor-in-chief, that there was too little specific technical information, too much redacted.

He wrote: "I understand the desire to contextualise and report things responsibly. However, I worry that you've been a bit too cautious. Without details about what is compromised and how (algorithms, companies/products, methodologies), people are left to wildly speculate without being able to effectively react.

"Please continue your excellent reporting; the detail given is adequate for a majority of the population. But the engineers and researchers who build and defend these systems could do a world of good with more information to work with."

I put this to James Ball, a member of the reporting team. He said: "We've withheld much less than people think we have. Many appear to have the impression we have the details of which chipsets, manufacturers, software products or encryption standards have been compromised, or how. We don't: as we said in the story, such details are held incredibly tightly, at a security level Snowden did not possess.

"The small number of redactions of the published documents don't relate to specific manufacturers, standards, or protocols, but some were made to address specific concerns of the NSA in the interest of responsible journalism.

"A huge amount of reporting effort, over several weeks, went into verifying and corroborating what is in the published story. There's a lot that's tantalising in particular slides, which can turn out to mean much less than it first appears. On Prism [the NSA's electronic surveillance programme], Tempora [a similar programme run by GCHQ], crypto [both agencies' efforts to defeat internet encryption], and more, we've been at pains to make sure we're as certain as we can be on what we're saying."

One reader criticised the Guardian for destroying computer equipment on which the details of the GCHQ files were stored; the hard drives and memory chips were deliberately wrecked after threats from senior UK government officials.

They wrote: "Not only [have] the UK proven themselves to be on the same level of being pathetic and despised the world over like their American friends, you as a news organisation have gone a step further. Your actions of destroying your own equipment due to pressure from your own pathetic government show what a true spineless coward you truly are."

Alan Rusbridger has explained elsewhere the Guardian's reasoning for doing this. It was a unique situation – the paper could either carry out what was anyway only a symbolic destruction (as there were other copies of the material in America and Brazil) to reach an accommodation with the authorities, or risk legal action that could have shut down coverage altogether and led to an expensive, uncertain court case. It's a fine judgment, but I can see why it was done.

One clear lesson of the affair is that if you are going to take, and release, a photograph of some of the debris left by the application of angle grinders to computer equipment, you should get someone who knows something about the innards of a MacBook Pro to write the caption. We said the bits pictured included a hard drive, but they didn't. That was still in a box, and a conspiracy theory was born that these weren't the real parts and the computers hadn't been smashed. They had.

One significant difference between the UK on the one hand and the US and Europe on the other is the lack of traction some of the Snowden-related stories have achieved among politicians and the public in Britain, which can be only partially explained by newspaper rivalry supported by a nudge from the DA-notice committee. Greenwald said: "I think part of it is that it is the product of the focus of the early stories: it was about the NSA and the US. That's the way it was defined. The NSA is where the focus was and the US where the reporting happened. Laura Poitras was reporting from Berlin and I was in Brazil. The UK got left out in the first couple of stages.

"The first story about the UK was about spying on the G20, and that was government on government, which has less impact and tends to interest people less. So as a first entry in the UK it was not ideal to engage.

"The second piece was about tapping into fibre optic cables under the sea and that was more successful. And then of course the Guardian had lots of problems with the UK government, plus lots of people in the UK who are pro-surveillance such as CCTV. It's just the way the reporting played out."

What gave the story fresh impetus in the UK was when Miranda was detained by the Metropolitan police at Heathrow. I asked Greenwald whether, in hindsight, he would have made different arrangements for that flight. On the face of it – given that six weeks earlier the Bolivian president, Evo Morales, had been forced to land in Vienna, apparently because it was believed that he may have been smuggling Snowden out of Russia – the decision to return via Heathrow seems risky.

"The idea that David was going to be stopped? I never thought it was going to happen. Guardian journalists much closer to the story had been going through Heathrow all the time. Laura Poitras had come to London to make a film and then returned to Berlin. The fact that someone so much more peripheral would be stopped didn't occur to us. The arrangements were made by the Guardian's travel agent normally. Obviously a mistake to go through London, sure, I wish he hadn't. They had so many more opportunities to detain people who were so much more involved.

"I was concerned when I didn't know what had happened. [But] I think the people most damaged by this are the UK and US governments because it has highlighted their behaviour. In a way I think it turned into a helpful episode because it highlights the willingness of these governments to abuse their power and attack press freedoms."

The investigation into the Snowden disclosures, involving dozens of journalists around the world, is an expensive one. What is it achieving?

Janine Gibson, the Guardian's US editor, said: "I think we went into this believing that there is a line between surveillance and privacy, and a necessary debate to be had about where that line should be drawn. It is clear that debate is best had in public, and public opinion, slow to shift in the US, has responded.

"A new poll published on the anniversary of 9/11 revealed that although 60% of Americans are still frightened of terrorism, nearly half think the government is doing a bad job of maintaining their freedoms. Nearly 60% oppose the NSA's collection of data on telephone and internet usage. Similar numbers oppose the secret Fisa court process that we have disclosed."

Greenwald is also convinced that a fire has been lit. He said: "I honestly think it has been so much better than I anticipated even. I have been writing about surveillance and the NSA for a long time, I started writing about this [in] 2005 when I began writing about politics.

"Surveillance doesn't always resonate with the public, it's too remote and too abstract. Even in the earliest discussions with Snowden he said, 'I have no fears other than I am going to unravel my life to talk about this [surveillance] and people won't care all that much.'

"Obviously it has been completely the opposite. There has been a sustained anger not just in the USA but around the world. There is a proper debate about the value of privacy and internet freedom and the dangers of state secrecy. This is exactly the issue I would wish to promote as a journalist, it is beyond my wildest dreams."

Some of the best stories in the Guardian's history – Suez, telling the public about British concentration camps during the Boer war – have been about campaigning journalism. Often that's telling people what they don't know they need to know.

Greenwald said: "I think it is the role of journalism to tell people what they should know and are not allowed to know. In this case, how vast a surveillance system is out there. Would it be better if the world remained ignorant of that?"