Basically the idea is that you assemble a Namecoin block and hash it, and then insert that hash into a Bitcoin block. Now when you solve the Bitcoin block at a difficulty level greater to or equal to the Namecoin difficulty level, it will be proof that that amount of work has been done for the Namecoin block. The Namecoin protocol has been altered to accept a Bitcoin block (solved at or above the Namecoin difficulty level) containing a hash of a Namecoin block as proof of work for the Namecoin block. The Bitcoin block will only be acceptable to the Bitcoin network if it is at the difficulty of the Bitcoin network.

The Bitcoin block chain gets a single extra hash when a merged mining block is accepted, and the Namecoin block chain gets a little bit more (because it includes the Bitcoin block) when a merged mining block is accepted. However, because of the Merkle Tree, the entire Bitcoin block doesn’t need to be included in the Namecoin tree, just the top level hashes (so the extra bloat to the Namecoin chain is not a big problem).

Since you make more money mining both Namecoins and Bitcoins miners will eventually all do merged mining, and the difficulty level for all block chains will eventually be the same.

Furthermore, the economic incentive to mine will be the combined economic incentive of all networks, making all networks more secure. Of course this allows competing networks (with different inflation rates) to quickly become secure. This subjects Bitcoin to more competition.

Ultimately the value of Bitcoin is a reflection of the need for Bitcoins to make exchanges. The more people using Bitcoin to make purchases, the more demand there is for Bitcoins, and the higher the price of Bitcoins goes. (Speculation also raises the price, but long term speculation is essentially a bet that the transactional demand for Bitcoin will increase in the future.) The higher the price, the higher the incentive to mine.

At any given time there is a certain amount of demand for a Bitcoin like currency to make transactions. That need doesn’t increase with more competition. That means that the transactional demand for Bitcoin is really the same as the transactional demand for all substantially similar forms of payment. As more currencies are competing to fill the same demand they actually reduce the demand for the other currencies as they become more widely used.

This means that ultimately, to the extent that currencies are interchangeable to end users, merged mining does not increase the overall security of the networks. The demand for currencies drives the price (and thus the value of the reward). Increased demand for any given currency results in decreased demand for others, lowering the incentive to mine for the other currencies. The total incentive is a function of total demand for all Bitcoin like currencies.

Except now competing currencies can market themselves as “as secure as Bitcoin but with lower transaction fees.” In other words there is a race to the bottom among competing currencies to offer the lowest transaction fees, because lowering the transaction fee doesn’t hurt the security of the network in comparison to the other merged mining networks. Users, following their own self interest, will adopt the currency with the lowest transaction fees as long as it has the same security of the competitors.

This will increase the price of the currency with the lowest transaction fee (because demand for the currency is higher), and decrease the price of the currencies with higher transactions fees (because demand for those currencies is dropping as it is being filled by demand for the competing currency). Because the currencies with the higher transaction fees were the ones generating the incentive to mine, overall incentive to mine will diminish. As long as a currency’s mining is merged with the freeloading currency, it will be powerless to increase incentives by imposing mandatory transaction fees.

The result will be a decrease in mining incentive, a decrease in mining, and ultimately all networks that allow merged mining will become insecure.