Recently, we've been reporting on the release of the deluxe edition of Ghost in the Shell, particularly its lack of a graphic lesbian sex scene that was cut from the original version, and has not been printed since Dark Horse's version of the graphic novel, along with some choice edits to additional panels, described in detail here. That situation remains the same in the new deluxe release Kodansha Comics, but the publisher reached out to Bleeding Cool to clarify exactly where the changes come from:

First off, this was not the result of censorship. The section was redrawn by the author, which is an important distinction. The goal of this new hardcover edition is to present the manga while respecting the author's intentions as much as possible, which is why we kept the right-to-left reading format and, most importantly, restored Shirow's hand-drawn sound effects (a first for an English edition of Ghost in the Shell). One of the questions we asked the author while going through editorial was which version of this passage he wanted us to use, and he asked us to use the redrawn version. I understand that it's not what some readers are looking for, and it's not the version that appears in the older Japanese editions, but it was the author's choice, not ours. We did not push him to choose the redrawn version, and would have been happy to publish the original pages if that had been his desire.

While a semantic argument could be made about the word censorship — in this case, censorship is not necessarily a bad thing, nor is it a free speech issue — the point stands that this certainly isn't Kodansha's fault, and honoring the wishes of an author is something a publisher should be applauded for, not derided.

That being said, the changes do have an effect on the story in the book aside from the simple lack of a sex scene, as Bleeding Cool's own Adi Tantimedh explains:

The censored lesbian sex scene actually has two humourous punchlines that the censored version messes up: Batou's physical reaction to linking to The Major's mind while she's having sex and having to punch himself to quell his reaction, and Kusanagi's girlfriends being pissed off at being pulled out in what's essentially cyber-coitus interruptus. It's part of Shirow's exploration of cyberpunk and virtual reality and its implications, so it's not as gratuitous as it initially looks. It also establishes firmly that Major Kusanagi is bisexual, possibly omnisexual, and therefore Queer. She's an LGBT heroine who's been stuffed back into the hetero closet by the censorship. The TV series hints she has girlfriends but doesn't come out and say it. You can also add that in the manga, The Major is shown having sex with her female friends while also dating men. There's a whole story about her dating a male agent from another antiterror agency. They inadvertently end up chasing the same case without knowing it and nearly accidentally kill each other in a friendly fire incident.

So if you're looking for an uncut version of the original book, even understanding that this isn't the way the book's author, Shirow Masamune, in channeling George Lucas, wants the book to be presented, you can always track down an older, out of print edition. But if you want to read Ghost in the Shell as its creator intends it today, with restored Japanese sound effects for the first time in English, then you can order the deluxe edition here or find it wherever fine graphic novels are sold.