The iPad's operating system iOS isolates files to an individual app, so other apps do not have access. So, for example, a book deleted from iBooks could not be read by another app because iOS does not allow one app access to another app's filespace. So it would not be possible, in a non-jailbroken iPad, to develop an app that could 'overwrite securely' another app's filespace - and neither could another app be used to retrieve those files.
If you're asking - at a hypothetical and theoretical level - 'does that deleted iBook still 'exist'?' then the answer is 'yes' and if you then ask 'could a very determined and skilled individual theoretically retrieve that deleted item?' then, again, the answer is 'yes'. But it's only likely that Government agencies etc have the necessary resources to be able to do that and so it's extremely unlikely that any such file could be recovered by a private individual.
Tim