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Those are drain holes. These are factory drilled holes. These are used in many applications some boat the holes are used in other they are just drain holes. No worries. These holes shouldn't go into the hull. The skid plate is added after the hull is built. So the holes just let water out of the plate itself.
If you are taking on water it won't be from these plates. The only way you will have leaks is a thru hull fitting or a crack in a weld.
Have you inspected the thru hull fittings and the hull for cracks.