Considering the velocity of the air that's moving downward into the throttle body, any and all protrusions into the bore are going to be disruptive. If you are gonna remove the plates in search of a bit more power, it stands to logical reason to eliminate as much protrusion in the bore as possible.
If I were to remove the plates, I would also remove the actuator rod and hardware and then plug the holes flush with the ID of the bore so as to present the smoothest air flow.