I haven't done any testing but can say from experience that drilling the hole will make a difference. It isn't a 'day light/dark' type of difference, but it is noticeable in a few instances.
Electrically, it's frequency dependent. The higher the frequency the 'better' a mag-mount -can- work. Deals with surface area and capacitive connections, which is how the things work.
Physically, count on there being wear marks from using a mag-mount over time, it will happen. Ordinary regular cleaning slows that wear down but can't stop it. It deals with how clean the air is, and it's never clean on a road/highway (fumes, dust, whatever).
'Fixing' a hole is 'relative'. How hard/easy it is depends on where it is and how big it is. If 'they' have to pull the head liner, count on it costing a bit more. And depending on how 'modern' the shop, sometimes you don't have to pull the head liner.
Drilling a hole can be traumatic! In most cases, it just isn't going to make a dimes worth of difference at selling time. I've also seen some vehicles that you just can't drill a hole in the roof (newer vans for instance), the AC ducting is up there. Who'da thunk it?
If you have the option, drilling the hole is the 'better' way of doing it. If no such option (for whatever reason), then don't.
- 'Doc