I think Perry knew. In the episode Dead Lois Walking, after Clark breaks her out of prison, he's talking to Perry, who is well-aware that Clark knows where Lois is and says, "I'm assuming I know you, son."

When I saw that episode, I figured he knew.

"Oh, you can’t help that," said the Cat: "we’re all mad here. I’m mad. You’re mad."
"How do you know I’m mad?" said Alice.
"You must be," said the Cat, "or you wouldn’t have come here.”

- Lewis Carroll, Alice in Wonderland