I've always found it interesting that people don't want to drill in a boat. Why would you care if mounting something (rails,etc). Holes are covered by device and if no chance of leaking who cares. Kind of like putting a bed liner in a truck, just hard on knees, doesn't drain well and when you trade in I never had a salesman say I would get less on a trade in because bed was scratched up.
Drilling in a boat
As the old saying goes, measure twice,
That’s the reference.
Well Gobbler to answer your question, and I am speaking from the fiberglass side of things , drilling holes in certain areas no matter how harmless it may seem , can cause things called cracks and they can become major problems later on in the life of the boat. There is so much force hitting the hull everytime you fly across a lake or river, hit a few waves and stuff can vibrate causing cracks and chips if the drilled hole is not done properly. That's just my experience.