Is Newsstand any more a folder than iBooks? Maybe I should ask that the other way. Is iBooks any less a folder than Newsstand? Honestly, I haven't really used Newsstand so I don't know how it works but I assume they are similar.
Edit: After playing with it for a bit, I now see the difference. I'm curious why Apple did it this way. I like the iBooks methods better.
I admit it's a bit curious having the two methods (I think that's because Apple has designed their UIs the same way, even though they behave differently).
But there are differences.
Newsstand is a folder. It simply launches apps. Newsstand apps are no different to other apps other than they have autosubscriptions and appear in that folder. So Newsstand itself isn't actually an app, it simply launches apps (some of which existed as separate apps on the score prior to iOS 5, such as New York Times).
iBooks, on the other hand, is an app that is not only the content organiser but also the reader (like iTunes is for music on the Mac). Each 'book' that you buy is not an app but rather just a document for iBooks to read. Whereas Newsstand is nothing more than an app launcher for special apps, or, as others have said, a glorified folder.