Hmmm. Can you post some pictures? I'm curious to see what you have, there.
Edit:
One thing I wanted to add... If this isn't a very large hatch, many manufacturers have been moving to using all composite construction. You can often tell by the 'finished' (or at least nicer looking than normal) and smooth appearance of the underside of the hatch. Given you don't see any telltale signs of a wood core, I suspect this might be your case. In other words, you may not have a wood core, at all. The "fix" could range anywhere from simply adding something like a nylon shim in the drip channel where the edge of the hatch rests to take the strain of being stepped on... to full reconstruction of the hatch and strengthening with extra glass such as 1708.
Going on the assumption that there is no core, it sounds like there simply wasn't enough support for the hatch when it is closed. Another option (to try and allow the hatch to be better supported when closed) is to put a spacer (assuming regular hinges) between the hinges and the hatch to allow the hatch to, in essence, sit lower and make contact with the floor structure.
You can easily/quickly check the thickness of the hatch with either a caliper or even just your fingers. A non-cored hatched is typically 1/4" to 3/8", or so, thick.
If these are, indeed, regular hinges... changing over to a full length piano hinge should also solve the issue.
Remember - gelcoat cracks do not necessarily indicate damage to the fiberglass underneath. Glass is much more flexible than gelcoat - meaning gelcoat will crack WELL before any damage to the glass.
And... where are the spider cracks emanating from? Just the screw holes, or other places?