In my 40+ years of owning motor vehicles and driving, I have NEVER had a vehicle lose it's value because of NMO mounts drilled into the roof, trunk, or otherwise. Matter of fact, I've had a demand for my cars from radio enthusiasts because they DID have antenna mounts, cables run, etc.
Car dealers haven't devaluated my other vehicles on trade-in because of mounts, rubber hole plugs, or otherwise where I had radios or antennas mounted. I did have someone mention where I had a magnetic mount which I never really liked; it took off part of the paint and the finish, and had remnants on the weather stripping where the coax came into the interior of the car.
Bottom line for performance? DRILL THAT HOLE, dump those magnetic mounts and enjoy your communications equipment when installed properly.