Since the hatches have gutters, the water that makes it’s way into the bilge is likely minimal. You could add gaskets, if you can find something thin enough that it won’t prevent hatches from sealing. A more likely culprit is the drains for fish boxes and storage, or a hull/ deck seam that needs to be caulked.
As for water in fuel, the first place to check is the fuel vent. The vent hose either needs to have a loop that rises above the vent or a p trap type vent fitting. Without the trap, spray can enter the vent and flow into the tank. A downward/rearward facing clamshell over the vent can help too.