One of these days, she’s going to make one of those intuitive leaps she’s so good at, and realise that Clark Kent and Superman are the same person. Actually, I’m surprised she hasn’t already done so.
Lois was concentrating on many things and did not imagine her work partner could be the Man of Steel. Let's also remember that Lex was gumming up the works just a little bit.
The series is so amazing.