This will be a lengthy explanation but it works to hide the books in iOS 9 iPad. Go to iBooks and At the bottom of the screen press on My books. You will have a bookshelf view of your books. Next press Select at the top right of your bookshelf view. Now select the book or books you wish to hide. An iCloud icon wifi appear on these books. Next, press the List icon at the upper left of your screen which looks like 3 lines. Your books, including the ones you selected for deletion will appear. Press Select again at the top right of this screen. Now select the books you want to hide that have the iCloud icon and choose to Hide iCloud books.
this will hide the books in My books and won't appear on the bookshelf. Make sure that the books you want visible on your bookshelf don't have the iCloud icon. If they do, press on the iCloud icon to download them. Trust me, this works. I was pulling my hair out trying to figure it out. Your hidden books will still appear in purchases and will never delete entirely. I guess that's so you can access a book you purchased without having to buy it again. I get it but they need to make it easier to hide them. Apple needs to create a folder in the MOVE option where you can store the books you wish to remove from bookshelf view. Then all you have to do is select and move. they can name it "remove from bookshelf" And "Return to bookshelf." Keep it simple. That's why I converted to Apple to begin with.