I think having a set spawn in one location would be easier as far as trying to find it and not spending hours upon end trying to find where it's at in the water.
Being able to damage boats and 'paralyze' them could be bad for PvP. All you'd have to do is paralyze someone's boat, field them, and meteor swarm or magical shortbow + the chain lightning special and kill mass amounts of people. It's a nice idea, but I can see some negative side effects to it.
I think a different idea that would work better, since you can be on your ship, and have it locked so nobody can get on, have there be a harpoon rope that you can shoot at the boat, which then gives you a tightrope, like the one in Fire Dungeon, and you've got say 10 seconds before it breaks. Giving you an access point from your ship to theirs and makes it so you can get on their boat using the rope, even though it's still locked.
As for gold dropping, as I suggested before, have there be a small island as well where some of the spawn starts, and that's where the gold can spawn when the champ is killed. The altar could be there as well.
I don't think this spawn would be abandoned...Depending on the difficulty level, i'd do it all day =)
Sea fights are a blast. I've encountered many over at Tera Sanctum.
I do think that efields shouldn't be able to be casted on boats/water to block people in. I think it's a cheap move =/