Oh, good poll, Kaylle!
I voted 'maybe', but I lean towards the view that Perry knows... and probably figured things out very early on. Certainly, I think his knowing is in keeping with his character. Plus, his knowing also explains why Perry allows Clark to disappear at regular intervals and with such flimsy excuses. What boss would allow that kind of behaviour otherwise?
The trouble with Perry knowing, and figuring things out early on, though, is that it makes Lois's ignorance that much harder to understand. She works much more closely with Clark than Perry and has had so many more clues... and it takes her
two years to figure things out! Doesn't Perry figuring things out before Lois make Lois seem 'galactically stupid'?
For that reason, I think both of them being oblivious works better for the overall workings of the show and that is probably where my doubts about Perry knowing come from.
As a (currently resting) fanfic writer, though, I will go with whatever Perry scenario works best for a story.
Chris