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My question is how long have you had the boat? If you bought it 2nd hand, the previous owner may have been checking for water in the hull or drilled the holes to let it dry out. Most vandals do not carry drills around and would likely done more than drill a couple of holes.

As far as patching, there are almost as many ways as there are members here. I would taper the holes and fill with a mixture of West systems with high density filler and maybe a little chopped glass. Smooth it out when applying and sanding if needed and a little gel coat, but that is not critical.