I was wanting to remove my side scoops for a cleaner look, but heard that the scoops on the GT/CS were drilled into the body? I was wondering if anyone could confirm that so I don't take them off and have gaping holes in the side of my car.

 

correct, sides scoops from the factory on the CS are attached using clips, so you will have holes.

 

You will need to bondo the holes, and paint