If you buy hatch inserts save the cutouts from your deck - you can use this material for the welding "filler" and to practice your welding technique. I recently patched a 2" hole in a poly kayak with good results using a heat gun, get one with a small nozzle to localize the heat as much as you can. I have also used a soldering iron to repair plastic. I never tried it on a boat but it might work well for screw holes. (try the practice piece first)
When I did my repairs I was able to get a piece of hatch cutout material and matching color welding rod free from the boat manufacturer. We wedged wood blocks behind the patch area to keep it from sagging when it got warm. After we welded the patch in place we used the heat gun to heat a wood chisel and smooth over the weld joint. The heated chisel worked like a spatula.

Don't overheat the boat when welding. If it starts to get too soft, stop and let it cool a bit before going on.

If you don't want to mess with welding, just put a pan head screw thru the hole with an acorn nut and some sealent.