Well, I always thought it was very believable that people could see Clark and Superman as different people - especially Dean's Clark and Superman. So, no, I don't think Lois was galactically stupid. But I do think it took her a little long to figure it out because Clark / Superman sometimes "slipped" up.
It seems I recently read or maybe GE'd a story where Lois knew immediately, but I'm not at home so I can't check right now.
