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I personally have had no problem with leakage thru any of my glass or similar composite bulkheads, in either of the two sea kayaks. They have both gotten hard use. I did get a bit thru the minicell foam bulkheads of my first, plastic, sea kayak. But ultimately all the bulkheads like that will leak at least a little unless aggressively maintained, and that is what dry bags are for. It is easier to find stuff if it is organized into dry bags anyway.
So the dryness thru the bulkhead part wouldn't swing me either way in terms of type of day hatch. Both the bucket style and bulkheaded means of getting a day hatch have the risk of leaking around the hatch cover seal/rim, so no diff between them there.
There are a few differences I see - you'd have to decide for yourself if they are advantage or disadvantage for your use.
The bucket style day hatch is likely to be more shallow, increasing the likelihood that someone like me of shorter arms can skip asking a paddling buddy to come over and rummage into the far corners of the thing.
It also holds less, increasing the likelihood that something you want on the water will end up in the larger fore or aft bulkheads... at which point you will have to ask your paddling buddy to come over and rummage into on of those compartments.
The two options are likely similar in how much weight they add.
I only see two major diff's between the two options.
1) The bulkhead, even one that leaks some, will provide added structural support.
2) The bulkhead, even with some leaking, will reduce the amount in of water that has to be dumped after a capsize over the bucket option.
For my own use, the last two make a winner. But that's me, you may have other criteria.