Nah, I don't think Perry knew a thing. I like seeing that scenario in fanfic sometimes, but on the show? Nope. Yeah, there were a lot of clues flying around (so to speak

) but Perry was drinking the same water as the rest of Metropolis (and Smallville!) and never figured out a thing.
Plus I really don't like the idea that Perry would put it together when Lois was still clueless. Really, really don't like it. So in my little universe, it never happens that way
PJ