iBooks for Mavericks is a complete mess. If you have a large collection of personal .epub files, not necessarily from the iTunes store, you are in for a world of hurt.
First, all of your files will be taken out of iTunes and their management will be brought over to iBooks. This is not an issue. However, iBooks lacks even the simplest of metadata editing, so you won't be able to change pictures, genres, names, authors, dates of publication or anything else.
Second, the files will be moved from your iTunes media folder to an obscure folder in your (now hidden) library.
Something like: /Users/~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books
They will be renamed from human readable, intelligent files into a 32-digit alphanumeric string. That .epub file will no longer be a file, but rather a folder full of .css files, html files, iTunes artwork files, iTunes metadata files, images and other content.
So if you have a copy of an .epub from Google, perhaps "Alice in Wonderland.epub" you will now have a folder in the above location called "C9F7853D6AC32AD3E43416BB47054D36.epub" that is filled with files.
From all appearances, instead of parsing the .epub, iBooks is converting it into a 'web page' of sorts. This also means that spotlight is now totally useless when searching for anything with an .epub extension. It also means that a spotlight search will now return a LOT more useless hits for short searches, especially if you have a large reading library (over a thousand here).
The parsed files are also significantly larger than the original .epub. Only an issue on machines with limited space, but still unnecessary bloat. My 3.7 GB library is now 6.58 GB, for example.
The reading mode is very limited, and there is no option for 'single page' in full screen. Overall the program is quite slow and extremely basic.
Obscuring, renaming and decoupling the users content within the context of the Finder is the worst possible solution. I highly recommend avoiding iBooks if at all possible. And if you are one to manually back up only select portions of your documents, I would also throw caution at you.
I'm glad I have a manual backup off site, because iBooks completely destroyed my book library.
And a final note, once you initialise iBooks, you can no longer use iTunes to manage your library, nor can you import books into it.
Stay far, far away if you don't use the iBookstore exclusively!
Update: Did some more digging. iBooks is unzipping, not parsing, the .epub files and creating folders out of each one. Hence the increase in space. However, the folder organisation was actually already present in the original .epub file. Still, it doesn't excuse moving, renaming or taking up more space....