As the underlying structure of an Aperture 'library' consists of plist files, xml files, sql databases and other Aperture specific binary files there is no reason to think a tool like diff would show no differences between a library and a vault.
Not to mention that one is a library and the other is a vault!
If the gear icon next to the vault update stuff is black then the vault and library are in sync. If you don;t trust the vault mechanism then just copy the library. Even then I'd be surprised if diff came up clean.
There's an interesting article on ApertureExpert about the differences between a vault and a library. Seems like they're mostly the same thing, I don't really know why diff would report a large amount of differences.
Aye Es Oh, I avoided to post that particular link, because I find it dangerous. I was wondering, if Rob de Jonge had read it though.
This is an implementation speciality, that may be true for a special Aperture version, but is not guaranteed to remain true for future versions. If Aperture would guarantee that a vault is an exact copy of an Aperture Library, the documentation would specify it that way. But it is specified as an incremental backup of your Library, so there may be many differences. Each time the Vault is updated only a part of the vault will change. The library can be reconstructed from this backup, but nowhere is stated. that the library and its backup are identical.