One of the things that I noticed on the show but which I've never seen discussed is Dean Cain's Oriental ancestry. His eyes without glasses have a slight almond-shaped cast to them, but with the glasses they appear rounder (at least, they do to me). Eye shape is one of the things we use to recognize people, and seeing someone for the first time after that person switches from glasses to contacts can be jarring, especially if the glasses are visually prominent.
It's as if everyone associated Clark's glasses with his face and mentally made them a part of him. I don't think Lois was stupid (either galactically or locally) for not making the connection. Even when she thought she was in love with Superman, she placed him in a completely separate mental and emotional slot in her mind where no one else resided, and since there was no comparison between Superman and any other man, she never compared Clark to Superman to see the similarities. It wasn't until Superman touched her with the same tenderness with which Clark had touched her that she made the connection.
Of course, Bob, you could read
That One Great Love , (my latest offering) where Lois figures it out rather quickly. It's a rewrite of the pilot with some twists in it.