Do PDF documents in iBooks get backed up to iCloud?
Yes, as long as you have the iCloud backup enabled your documents will be backed up. I have first hand experience. After exchanging a defective iPad the new one, after entering my iCloud account information, had all my books (both epub and pdfs, I don't buy books from the iTunes store because of DRM), links, gamecenter data, and application data.

What didn't synchronise was music and videos.