Terry,......You have normal concerns..(

), but there are a lot of boats will drilled holes. Here is the secret. Drill only a hole size necessary for the screw to fit snugly. Use an epoxy or resin filler to help plug the hole as you put in the screw. Boat shops have this in a tube.
You could epoxy a plate to the boat for ducer bracket mounting. Be sure to lightly sand the area first and then repaint around the added plate.
Of course if the boat is metal then maybe screws and epoxy are the best.
Maybe some of the guys will add to this with pictures.
Chuck