I am assuming you mean the fans would move the air from the bottom out the top versus from the front of the case to the back.
I would for see cons being: reducing room for other components (depending on how large the heatsink + fan is), reduced temps.
You are probably going to want to stick with the time proven method of having the fan blow across the radiator from the front of the case to the back because it directs the air directly into your case exhaust fan, on top of the you aren't grabbing hot air coming right off your GPU.