Well, it is a new twist that Lucy figured Clark out, but it makes sense if you stop to think about it. Lucy has been spending a lot of time with Clark, which means that he has pulled his disappearing act on her at least a few times. Since Lucy is coming into this with fresh eyes, as opposed to Lois's anti-Clark prejudices (which are really self-defense against her own attraction to him), Lucy is a) less likely to write his odd behavior off as 'that's just so Clark!' and b) once she starts to think of it, more willing to accept the idea that Clark could be Superman because she hasn't got him in a preconceived hick category in her mind.
It does seem that Clark is being a bit of a doormat to let himself be manipulated into seeing Lucy so often, but, given how he responded to Mayson when she pulled something similar, it is in character. That boy has got to learn how to draw some boundaries with pushy women.
I will admit that I, too, was surprised that Clark fessed up to Lois so quickly, but this is even better than the jealous Lois that we were all expecting after the first part. You've refused to go down the predictable path and brought in a whole new level of complication, and a real reason for Lois to be truly jealous. Lucy is playing with fire, but that, too, is in character. It's a good thing Clark is in no danger of falling for Lucy, or she would be guilty of leading him on as well.
Looking forward to seeing what twists and turns you take with TOGOM.