I've installed deck ports in my H16 and the overall thickness of the top deck is about 7/16". There is no contact between the fiberglass layers, so the foam is an integral part of the sandwich which creates the strength of the hull. Your idea of using spray foam has been discussed before, but I've never heard of anyone following through with the idea. If your boat is as bad as you say, I don't think you can hurt anything to try it out. I think the key will be to get a clean surface for the new foam to adhere to.
Another idea is to pick up another Hobie that has good hulls, but is missing other parts. It might be cheaper in the long run, if you consider all the work and swearing that you'll be undertaking.
Good luck. Keep us posted on your progress,
Jack