If the purchases are hidden then they should not appear in the purchased section of iBooks, so I'm not sure where you are seeing this. That's whole idea behind hiding the purchases, so they do not appear in the purchased tabs of the iStores.
In iTunes on your computer, sign into your account from Store>View Account. You will have to enter your password. Click on Purchsed under Quick Links on the right side of the screen. Then click on Books in the next screen. Hover over the book that you want to hide and an X appears in the upper left corner of the icon. Tap that to hide the book.
If you have done that - Have you closed iBooks completely and rebooted the iPad? Sometimes closing and restarting forces the app to refresh.
Tap the home button once. Then tap the home button twice and the recents tray will appear at the bottom of the screen. Tap and hold down on any app icon until it begins to wiggle. Tap the minus ➖ sign in the upper left corner of the app that you want to close. Tap the home button twice.
Reboot the iPad by holding down on the sleep and home buttons at the same time for about 10-15 seconds until the Apple Logo appears - ignore the red slider if it appears on the screen - let go of the buttons. Let the iPad start up.