I agree with KatherineKent that this must be the real Superman. He's got to be bugged. It's probably built into that new suit of his, along with some sort of GPS tracker, probably. I like Virginia's idea of kryptonite in the suit that they can threaten to release in order to control them. That's incredibly sinister and much more effective than just having a hostage.

I wonder if he thinks that since Lois is in touch with Martha and she's asking him about Clark that she must know who he is?

Lois and Martha must have never discussed Jason and what happened with Zod. If Lois let slip to Martha that she thought that Jason might be Superman's, I imagine that Martha might have told Lois that he's Clark so that she could be acknowledged as Jason's grandma.

"It is a remarkable dichotomy. In many ways, Clark is the most human of us all. Then...he shoots fire from the skies, and it is difficult not to think of him as a god. And how fortunate we all are that it does not occur to him." -Batman (in Superman/Batman #3 by Jeph Loeb)