Probably not bound by it because it's a contract. Any contract (such as an NDA) that is contrary to public policy (such as keeping criminal activity hush hush) is void on its face. It would be an issue the court has to take up.
Adding that the NDA probably doesn't explicitly state that knowledge of criminal activity is not to be disclosed. So he either violates it if Mueller is that dumb to include that or since it isn't covered by the NDA and Flynn knows it, then he can run his mouth all he wants. Mueller might war with him but Flynn will win.