ports require special harbours you can't just plop one day whereever... i would imagine that if it was to be realistic that the current trade ports are optimal and realistic...
And i think you would be more worried about securing trade opportunities and managing your fleet than figuring out which port to take over...
the bigger your fleet the more you have to trade, more money you need, more captains more stuff.. more more more... you have a 200 year period
each port you take over you neeed more money to manage it for upkeep and need to have more marines and ships garrisoning/patrolling, because the bigger you grow the more enemies you naturally make, the more your trading the more valuable your trade ships are to raid.. i feel that once you've taken at least 5 ports or so you'll have your hands full managing cash etc.