Re: This may be a dumb question...
Overtime, the screw will work itself loose and start to back out due to the vibration of the boat. If that happens, your glassing could be jeopardized and water might be able to seep through the hole and start rot. I don't like to have any areas of bare wood that would or could be exposed to water.
Again, that's my opinion. You are more then welcome to leave the screws in but I would definitely make pilot holes and add some pb or 5200 before running them in just for insurance.
By the way, not a stupid question.