The standard 8″ hatch in the deck is OK for putting small items and a small dry bag below deck but not much use if you need to store anything larger and want to avoid damaging the plastic thread of the hatch.
There are larger round hatches available but they still have the thread issue.
The only hatches which claim to be fully waterproof are made by Armstrong Nautical and are available in 6, 8″ and 10″ round or rectangular shapes.
Others have used yacht-style hinged rectangular hatches which give good access but may be a bit heavy.
Another alternative are Kayak hatches which are designed to be 100% waterproof if the kayak turns over. This article has some useful information on the various types available and their maintenance.