The iBooks app has been known to disappear after an update, for some obscure reason.
Try a reset.
If it still does not come back go to the App Store and download it again. Visit the iBooks Store in the app and select the Purchased tab. You'll find all the iBooks you've bought ready for download again.
Reset: Hold down the power and home buttons until the Apple logo appears. The iPad will reboot. This usually takes a bit longer than a restart.