Also, not a bad guy, but Star could have known. Clark had told her, when hypnotized, that his name was Kal-El. When he was in court as Superman, he gave that name. If she put two and two together, she would get CK=S.
Finally, IIRC, most of Smallville would have had to have known after the NK story arc. Nor very publicly tells Clark, who is dressed as *Clark*, not as Superman, "I want your throne, Kal El." The few Smallvillians(?!) who hadn't been present would undoubtedly have found out about it from those who were. So if you wanted to create your own villain, you could make them a citizen of Smallville.
I must say that Clark's alter ego is one of the worst kept secrets there is. And the fact that it isn't universally known in the L&C universe is another of those instances where you have to suspend a lot of disbelief.
Joy,
Lynn
