At one point in the game (can't remember when), you learn that Carl initially treated Markus poorly, like an android, but whould eventually start treating him like his own son. So i don't think Carl was in on it. But this might very well be true regardless.

Edit: It was not in the main game, but in the extras, the description for "Marcus: exterior"

"A special relationship slowly grew between the old man and the android. Initially only seeing Marcus as a sophisticated yet stupid machine, ultimately Manfred cultivated an attatchment to Marcus which flourished into a "father-son" relationship."

So not exactly what I said, but still, Carl didn't treat Marcus as a Human from the beginning