Thanks, Lieta and Sara!
Lieta - Superman can't blow his cover to Lois just yet. There's still 30 chapters yet!
Sara - Okay, here's my reasoning for why Clark was found naked and Superman was not. I'll admit it's not consistent with the show, but I think it's supportable.
Clark was wearing regular clothes, dark, but normal clothes that would be somewhat loose on him. Superman was wearing the skin-tight suit.
My argument is that Superman's suit was protected by his aura, but that Clark's clothes (which were further from his body) were not.
And while I honestly can't remember for sure, I think we're pretty far from a conversation between Clark and Superman of the type the two of you are speaking.