It looks like the iBooks Library function of iTunes have moved to the OS X version of iBooks. Add, delete, and purchase your books using this app; though you still have the choice of purchasing them through iTunes.
Syncing of iBooks to iOS devices is still in OS X iTunes. Connect your iPad, select it, and go to the Books tab. You'll see you listed books and the same old choices of syncing all or selected books.
People have been complaining that OS X iTunes is too complicated, trying to do too many things at once. I suspect that providing iBooks as a separate app but leaving syncing in iTunes is Apple's first step in breaking out all the features. I expect that the stores and iOS syncing features to stay in one app while the various player/reader apps will become separate, while still providing access to their specific store sections.
Maybe be the all store function will be removed from iTunes when there is an app for each type of media.
Kind of like it is in iOS.
Of course, I'm just speculating.