How can I sync my iPad/iPhone with iTunes except for the apps/iBooks?
The reason why it's asking you to transfer purchases is because your Mac doesn't have the apps (and the data associated with said apps (e.g.: game data, documents, etc).) on file on the computer. When it's transferred, it can successfully back it up without losing your data.

As far as I can tell, there is no way around it; you are going to have transfer the files. After that, go to the "Apps" tab on your iPad section of iTunes and uncheck it. This should stop syncing your apps. Do the same with the "Books" section.

As for the question of whether or not your apps and books are on iCloud, they are. Every song, album, music video, TV show, app, or book that you have downloaded is associated with your Apple ID and can be re-downloaded for no extra charge.

I hope that this solves your issue.