There are a couple of options. Hobie currently has plastic welding rod available at
no charge in the various colors. It can be requested through your local dealer (who may or may not know about it). Otherwise or until then, you can just put screws in the holes with a dab of clear silicone calk to seal them (optional). This will make them look neat and keep the holes available for some possible future use!
If you're welding holes, you can use any matching plastic strip (about 1/8" across). Melt the tip with a lighter and dab it into the hole; quickly flatten it out with a putty knife or flat blade. Practice first till you get the hang of it!
PS: When ordering the free welding rod, provide the year model as well as the color for best color match. The colors change slightly over the years so an exact match is not always possible. They can at least get you close to your original color.