If it were me I would cut a round plug from your extra material left over from adding the hatch, chamfer the edges. I would then order the Kayak repair iron and material kit from Hobie, then carefully fill around the bead from the bottom up layer after layer (like weld beads). On the inside of the hull I would continue building up around and over the repair about 3/8 inch wide when your done and humped up on the inside about 3/16 high. Be very careful not to let the area around the welding overheat (basically take your time). I would then take a 5 inch diameter piece of PE (something like a cutting board) and dope a thick layer of silicone (probably half a tube) over the patch area then press the PE plate over the whole works inside the hull and let it dry. The PE plate protects the repaired area from bending and flexing inder normal conditions. Plus if the seam leaks water, the silicone will contain the leak. It might be ugly from the inside, but you will only see the 2 inch dia ring where the repair was made from the outside. Everything should match colorwise. Of course can you probably skip the plate on the inside, but keep in mind it will always be weaker than the original hull in that area. At least thats the way I would approach it.
If it continues to be a problem, I believe Hobie has can supply replacement hulls for out of warranty boats for a reasonable price plus shipping (much less than a whole new boat). I have a friend who did that with his AI and I think his was around $500 plus shipping (but don't quote me).
Hope this helps