She doesn't know in ATAI until Before she was put into the freeze. There's still a chance she might learn before that. There's at least one point in the show that would have been easily figured out (when he went to tell her in the morning.)

CLARK: No. I'm just worried I'm a jinx.
JONATHAN: A jinx?
CLARK: Yeah. Let's face it, ever since she's known me, Lois's been kidnapped, frozen, pushed off buildings, almost stabbed, poisoned, buried alive and who knows what else, and it's all because of me.
-"Contact" (You're not her jinx, you're her blessing.)