I have thought after reading some books on the subject of leaks that it may be easiest to split the boat up into parts. Say, three. Pick a point at each of those parts where you can pour a little or a lot, of dyed water. Obviously the dye should be washable and water-based for easy clean-up and to avoid staining. Use a different color for each part of the boat.
I think that if you used that method you could quickly narrow the search for where the leak is coming from because the dye colors would tell you what part of the boat the water is coming from and where it is possibly leaking in to. Again, I just brain stormed but in mechanics it appears sound with the biggest conern being preventing staining.
Other than that, if you think it is the Hatch
you could put water guards around the top of it to stop most water from reaching the hatches
gaskets/seal. While it wouldn't "fix" the leak it would probably cut down on it until you found the culprit anyway. Besides, Water guards around hatches
and such are usually a good idea anyway as they protect the seals from the tremendous force of wave to hatch
action. Sort of like how Barrier islands absorb the worst blows of a storm.