Your idea of using a fish tank pump is not a bad idea but due to the size of your ship/ ballast requirements, it would take forever to fill and empty. Have you thought of using a bilge pump from a real boat. They will pump water a lot faster and run on 12 volts.

For the straight hull sides, have you thought of using 1/8" door skins. Cuts down on construction time, use the foam for the curved areas of the hull.