Doesn't a solider tell the general / coronal that "that's what they're calling him now" during the Smallville battle sequence? If so, Lois wasn't privy to that development since she was taken at the same time as Clark, so she doesn't know that she should call him Superman, she only knows him as Clark.
IIRC, this is said when Lois, Clark, and the Colonel show up at the base to talk to the General (was he a General?) about a plan to send the Kryptonians back to the Phantom Zone. As I understand it, the Colonel (or whoever spoke to the soldier on the phone) got the name "Superman" from Lois (or possible from Clark, but he got it from Lois).
