I was under the impression that any apps that you currently had on your iPad would work with the new updated iOS. However, I can't remember why I even think that but I probably read here on this site.
In any event, I believe the overwhelming majority of your apps should still work even if some will not under the new iOS. What I'm saying is that there may be something else going on that will require something additional on your part - perhaps restoring your device to factory settings and then restore to your backup.
iBooks is an Apple App but there are other reasons why the apps could be crashing. You could try closing all of the apps in the recents tray and restart and see if that helps, but you may need to restore your device(s) if nothing else works.
Go to the home screen first by tapping the home button. Quit/close open apps by double tapping the home button and the task bar will appear with all of you recent/open apps displayed at the bottom. Tap and hold down on any app icon until it begins to wiggle. Tap the minus ➖ sign in the upper left corner to close the apps. Restart the iPad. Restart the iPad by holding down on the sleep button until the red slider appears and then slide to shut off. To power up hold the sleep button until the Apple logo appears and let go of the button.