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In my opinion, any of the above methods could be used to repair a 3/8" hole. There are also many more methods you could use, some more skill-intensive than others, and some would certainly be more involved with the determination of water intrusion.

You really need to look at these holes closely. Are there blisters in the fiberglass at the edge of the holes? This is one observation that would definitely change your course of action in the repair process you choose, and there would be a different repairs required for different observations of the problem. If it's just a couple of holes, that's one thing.

Others here have asked questions in their replies that reflect their own experience in observing holes in hulls. You need to look at yours, take some pictures, then review, with a search of this site on "hull repair", in order to determine the best way to attack your possibly unique problem.

I am in agreement with the poster who questioned vandalism as the cause of your problem. I have NEVER heard of a vandal drilling holes in boats, doesn't mean it couldn't happen, but it would seem that vandals would be set on doing damage in a much easier,(for them), way. Have you made someone that angry with you lately? :) Have you had the boat in a bad area of town full of out of work craftsmen carrying around battery powered drills? :)

Are these holes in the bow of the boat? My 1989 Whaler 27 has 2 holes approximately 3/8' that appear to be drilled into the bow of the boat with no trim that are actually the anchor locker drains. I would certainly not want to fill them with anything, as the anchor locker would not drain if they were filled. These holes were made at the time of manufacture of my boat by Boston Whaler, and they have served a needed purpose every since then. Have you determined if the holes in your boat could actually have been drilled on purpose by Boston Whaler? I am unfamiliar with your model of Boston Whaler, but be certain they are not supposed to be there before panicking. :)