Joan: Yes, that's true, I didn't mention to whom Clark did his big reveal.
Clark has come clean with Martha and Jonathon!
They're his new dimensional folks. Lying to them is twice as hard as with Lois.
I thought Lois had overheard the entire conversation when it was only Jonathon's cover story suggestion. So Lois doesn't really know the truth.
She knows that Clark is Clark and that he was orphaned at a young age.

One of the morals of this story is never believe something overheard without outside cooberation.