I remember seeing somewhere that a new keypool is created after you encrypt your wallet, but I can't find it anymore. I also can't find anything like that in the code, but it's quite possible that I'm looking in the wrong place.
I just tested it, doesn't seem to be the case. I created a new wallet, backed it up, encrypted it and reloaded bitcoin. I then generated a new address using the new encrypted wallet and then the unencrypted backup wallet. They both generated the same address.
I think this behaviour is expected, otherwise old backups would be invalid after encryption (EDIT: of course "invalid" is the wrong word here, they would just cease to be future proof). There are a lot of people who don't take snapshots that often and rely on the keypool.