Epoxy should be just fine for small holes. It is very commonly used in fiberglass repairs. Yes, it can be rather brittle, but there's not much movement in a little hole and the filler helps there some. (Fiberglass construction actually is the fiberglass proper held together with or embedded in some sort of resin, polyester resin being the most commonly used one. Epoxy is occasionally employed as the resin.)
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West System epoxy people have some pretty good, comprehensive information on fiberglass work and repair techniques available. The West System products are also quite good but fairly spendy.