If someone were going to start attacking MtGox accounts, they aren't going to steal 29 BTC, et even worth the attention it brings... 2FA works fine, the OP enabled 2FA after attack. That simple.
He is claiming otherwise. Although you are right, we would probably see evidence of more 2fa heists if the OPs claim is true. Perhaps this was a test run. Perhaps it's just a gox troll.
Logs would be nice (from gox), at the very least. Perhaps you can pull logs from the yubikey, idk if that is at all possible. In the end of the day the logs could be tampered with by either party so there is no way to know for sure.
If this is a lie by the OP we would need to find motive, perhaps another exchange spreading FUD.