I think it would be a nice addition to have Faction members occasionally seen sailing around the sea of thieves.
Occasionally a Kracken or a skeleton galleon will attack them and upon saving them they will reward you with some gold.
...or you can attack them and take the loot of their respective faction.
They will also serve a valuable purpose, that being camoflage.
You see a sail and you know its a player and likely hostile.
However the seas are littered with friendly ships so now when you see sails you are unsure, is it an npc or a player?
Plus, if you use the harpoon rowboat its a cool way to get around grappling a vessel and using it as a way to get around.
Dont board though or the crew will attack you.
They respawn like skeletons only much slower and if you kill all the crew the ship will sink.
Players who actively engage friendly npc ships will incur a bounty and will effectively have a reapers flag for x amount of time, rewarding players a monetary value upon sinking them as a deterrant. Plus, these player ships marked by this reapers mark will likely be loaded with loot.
I think if anything it will make the seas more alive too.
