I would totally discard the idea the it might be intended as ballast in a boat of that type.
Not so sure the proper term for what you have is a thru hull, which may throw off those who try to answer your post. Sounds like a simple cocpit drain.
There should be NO water in the hull. Please clarify whether you mean there is water in the cockpit or the hull.
If all you have is a cockpit drain that lets water into the cockpit, just plug the darn thing and carry a small bailing bucket or a large sponge with you.
If water is entering the hull, either through a faulty cockpit drain or some other point, the leak must be found and repaired. I would hope that the hull is NOT filled completely or even partially with some type of foam, as I have seen foam get waterlogged and drying it is difficult. If that's the cace, the boat might have to have it's deck removed to make the repair
So, please clarify where the water actually is, and whether you've been able to remove it after sailing.