I think the moment that sold me on Perry knowing was in Contact when Perry said the following when Lois said she'd been abducted by aliens:
"Now, I don't know what it was, but I know you, and you wouldn't lie... at least to me... most of the time... so forget about the airport story for now; you can turn it in later. Whatever happened, I want you and Clark to get to the bottom of it, okay?"
So Perry knows Lois is lying to him about something and seems remarkable okay about it...Perry the old newshound wouldn't ordinarily let something like that go!
