For one the loot isnt too good compared to fort raids, so maybe the numbers could be adjusted a little to match the gold.
Yes there are items on every ship you sink, but in my experience, there isn't time between waves to pick up the loot from the ships, a lot of it just sinks. All of the loot should be dropped at the end of the wave on a row-boat with some type of smoke to show where it is for the crew.
The loot in my opinion should be worth more than fort raids and right now its less. Objectively it is much easier to do a fort raid than a skeleton ship raid. You have to use tons of cannonballs and supplies to sink every ship, where during fort raids, we run around with our infinite sword swings and don't need to use any supplies except for food which you find on the island.
The skeleton ship raid loot should be adjusted to resources used/difficulty.
