Well, I think that Perry knew for sure. He got the first big hint in season one (or was it the pilot even?) when Clark claims to go after Lois and Perry finds him in the closet in front of an open window afterward. Add the flimsy excuses and Clark's unusual behaviour during the heat wave, and voilà! CK=S

The only known quantity that moves faster than
light is the office grapevine. (from Nan's fabulous Home series)