I've gone around in circles on this question for awhile but finally went
with the internal bungie hold-downs as shown in the links at CLC. Here is
another very clever idea for hatch hold-down posted here previously:

http://www.kayakforum.com/cgi-bin/Building/index.cgi/noframes/read/172323

But whatever you do, I think it is advantageous to include some more positive
system for retaining the hatch, it could be a real unpleasant experience
should the hatch come open out on the water in rough conditions. There is
also the issue of possibly losing the hatch or having it flapping around
while carrying the kayak on a roof rack in high winds.

While there are many clever ideas that would likely work great in calm
waters and gentle conditions, and would also be generally easier to
handle opening and closing, I think it is worth thinking about what would
happen in a worst case scenario, and whether the hatch and integrity
of the watertight compartment would be retained.

--
Ogata (eric)