I wonder why Lois Lane has special status among all the other friends and co-workers that are just as close to Clark. When Lois suspects the truth, Superman comes up with ways to prove that he and Clark are two different people. So why beat up on Lois Lane? Usually when Lois gets a lot closer to Clark (i.e. sleeping with him, married to him), she already knows his true identity.
For all we know, Clark and Superman do look different to everyone in the comic book reality.
Look at the two guys in this picture. How do we tell them apart and know that they're not identical twins?
Well, one has hair flopping in his face, while the other has hair slicked back. One has his eyes obscured by a mask, while the other you can see his eyes. And they're each wearing distinctive costumes. Otherwise they would look virtually the same.
That's how a lot of comic book art works. There are a few artists who do incredibly detailed, photo-realistic art--but most comic art is about simplifying details and getting an image down to its essential elements. And most characters fall into types, distinguished by basic details like glasses, hair-styles, hair colour, facial hair.
For most comic art, Superman and Clark do look different. I can say that, most of the time with most artists, they always did appear like two different characters to me. I'd have to remind myself that they're actually the same guy--but I know that only because I was let in on the truth (thus Clark's wink to the reader at the end of a story). If comics were written so we never saw that the two characters were the same person, maybe that wouldn't be so obvious.