I would be more concerned about the condition of the remainder of the hull bottom than the holes. If the structure of the remaining hull bottom is good, the holes will not reduce the structural integrity of the hull much. Turn the boat upside down and press in all over the bottom of the hull. If the hull feels soft and spongy, I wouldn’t waste a lot of time repairing it.
It the structure seems good, how to repair the boat depends on how much time and money you want to spend. It sounds as if you are inclined to do a decent job. If that is the case, I would fill the holes with G Flex epoxy thickened with some silica gel powder. The G Flex will do a much better job of permeating into the interstices of the foam core than most of the various “goops” you could use. Once cured, the G Flex can also be sanded to a fair and flush surface with the rest of the hull. You can buy a kit containing a small amount of G Flex resin and hardener, some mixing spatulas, mixing cups, and silica powder, dental syringes and a few other sundries for around $30. This will probably provide enough epoxy to fill the holes. In addition to this, you will require some clear packing tape, sandpaper, some additional disposable gloves (besides those that are included with the kit), paint that more or less matches the color of the hull exterior and interior, and a few other things like paper towels.
I would first get rid of whatever has been used to fill the holes and gutter out each hole on both sides of the hull, beveling the edges of the holes so that the cross section of each hole will have an hour glass configuration. This will increase the surface bonding area for the epoxy and also get rid of whatever was used to fill the holes, which could potentially interfere with epoxy bonding. If you happen to have a Dremel or similar rotary tool, it can be used for this process but sandpaper will work.
Depending on how the holes are distributed on the hull surface, you may not be able to fill all at the same time. Position the boat so that the epoxy mix will work down into the holes by gravity and back up the holes on the inside with clear packing tape to contain the epoxy. The G Flex can be mixed in small batches in a 1:1 volume ratio (resin to hardener) by eye, then stir in some silica powder to thicken it moderately. Dental syringes can be filled with the epoxy mix and are convenient for getting the epoxy down into the depth of the holes. You will probably need to make at least two applications to completely fill each hole as the epoxy settles down into the foam core. Continue until all holes are filled on the exterior at least flush with the surrounding hull surface. When the epoxy is fully cured, you can sand it fair and flush with the surrounding hull surface. Inexpensive white vinegar that you can buy by the gallon at the grocery store works pretty well for cleaning up mixing spatulas, cups, and dental syringes after use.
After filling the exterior side of the holes, you will need to turn the boat over, remove the packing tape, and repeat the same process on the interior side of the holes. Once the holes are filled, paint over the epoxy on both sides of the hull with a paint that more or less matches the color of the surrounding hull.
