It should, but it won't be user accessible as an individual backup. You would have to restore the entire iPad to get back lost data. iTunes only keeps your very last backup, so restoring can be tricky. For instance, if you lost the data, synced the iPad, then tried to restore the data it would already be gone because you overwrote the backup. And iTunes always does a backup when it syncs, and unless you change the preference it syncs (backup first) when you connect it to the computer.
This is the only reason I do not recommend Bento as a stand alone database. It's great if you also have Bento for OS X (you can sync between them), otherwise your data is stuck on the iPad, and lacks a robust/secure backup.
Bento is supposed to be working on some DropBox integration. No telling when/if that will happen. Uuntil then I would not use it to store important data.