Not that hard to miss. I mean, who thinks a guy like Superman would even have a secret ID, he doesn't even wear a mask. Add the carefully crafted characteristics of Kent, plus the many times she's seen them both together at the same time because Supes got J'onn or a Superman Robot to pose as him to throw people off that were getting too close, and it's no wonder she, or anybody else with the exception of the Bat, didn't know about it.
Besides, MJ still wouldn't have known either. Even after he told her.
Too busy cutting herself and spending up all her dough I guess.