How Do You Fill-In Unused Through-Hull Holes?
You seem to be asking two separate questions. The first is how to remove a thruhull and fill the hole and the second is how to fill a smaller bolt hole in the hull. With the larger hole from a seacock I prefer to grind out a large tapered (8:1) area from both the interior and exterior of the hull and build up multiple layers of epoxy and cloth from both sides. I have nor problem with using thickened and reinforced epoxy as a core between the inner and outer cloth lay-ups on a really thick or cored hull.
For a bolt hole sized hole I would fill it with thickened epoxy and then grind a small dimple and cover the hole with a layer of cloth and epoxy. The cloth increases the tensile stength of the repair and prevents shrinkage from causing a leak into the inner laminate.