I think i know why there are no merchant ships in the carribean..

[Captain Del]

There were actually plenty of other smaller companies that resided within the Caribbean, though not as nearly prominent as the East India Company, like the Dutch West India Company.

I'm guessing the reason they don't want to open up new merchant ships to plunder, is because then they may be obligated to create a whole new brand of enemy in the game - also meaning the revisement of many quests, the opening of many new quests, new places, etc., all of which one update probably can't handle.