While the OP has a decent idea or concept, I believe that it simply opens up doors for greifing or resource locking players out of enjoyment. I am posting the points addressed and then offer some questions to them.
-- "While being pursued, 3 people from the lead ship jump into the water and try to grab onto the pursuing ship's ladders as they chase. If they miss, it doesn't matter, just mermaid back."
There is a negative consequence to this. Have you ever tried to man a galleon solo? with the lack of hands it allows the other ship a chance to close the gap while chasing them and attempt to board/attack the single man left on the galleon.
-- "Lead your pursuers astray by sailing past an island while you jump off, letting you ship sail off into the sunset. When out of sight, scuttle ship to respawn it, take mermaid back."
Now this one is interesting as I have done this very thing while playing solo. So if I manage to outsmart a galleon then I should be penalized for it? If a sloop has no chance of getting away from a galleon, and they have to pay for scuttling their ship, eventually they will be resource locked due to repetitive attacks.
-- "If you're ship gets stolen, no worries, just take the mermaid teleport to it. If the enemy crew kills your crew, no worries, just keep respawning on your ship. Or just scuttle it."
Again, what happens if the person is new, they run out of souls or money to pay for a new ship? does the attacking crew get to keep the ship while the single person is left stuck on an island because they now have no ship within a game that is based around sailing?
-- "Ran out of planks and cannon balls? Just scuttle and respawn a new ship."
If you run out of cannonballs and planks, odds are your ship is about to be sunk anyways from whatever battle you are in where you ran out of said balls and planks to begin with.
There is risk in this game, it comes from treasure chest. The risk you choose to take comes from HOW MUCH treasure you plan to carry on your ship at a time. Do not want to risk a lot? only carry one treasure chest at a time. Want to risk a lot, load your boat to the sails with chest and see if you can make it back.
Putting a 'life currency' in the game will give griefers the opportunity to do what they do best, grief. If souls are put into the game, I can promise that there will be groups that seek to limit the souls others can collect, ultimately leading to a huge imbalance of power.