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The foam in a whaler absorbs water very slowly. Depending on where the holes are and the angle at which they were drilled, water could have been under pressure in the holes and you may have some wet foam. You didn't notice the boat sitting lower in the water so the intrusion is probably minimal and shouldn't be a big concern. As for repair, there will be as many different opinions as members on this site. 3/8 inch holes could be filled with 5200 and the boat used the rest of the season and repairs made after you winterize. Do you know how deep the holes are? With that information I would cleanup the holes, get a piece of fiberglass cloth, the width equal to about 1/8 inch less than the hole depth, wet it out with epoxy and roll it up and stuff it into the hole. Finish off with a dab of gelcoat and forget about it.