It was his name.
Bond turns round and says that Mathis wasn't a very good codename purely because it was his real name.
That was my impression too. Have to watch again to be sure,though...
I'm not sure about that... If so, why use "codename", instead of "cover name" or "alias"? And it would make better sense if Bond simply told him "Mathis wasn't a very good codename", without first asking him IF Mathis is a codename. Wouldn'it?