I think there are some really good ideas here.
I haven't been playing the game very long but have become frustrated with my attempts at trading, which have been driven by my attempts to level up my crafting skills. I'm still learning the ropes (nautical term intended).
I've been traveling up and down the east coast of the US and have not seen the huge price fluctuations that you mention. However, I do not understand the mechanics that drive price change. Scarcity should raise prices and glut should depress them; it seems that the selling price of a resource rarely reaches the buying price, even when there is none to be had. That needs to be fixed.
Trading ships are just too big. The cutter has a capacity of 60, but the Trading Cutter a capacity of 1200? Now, carriages and guns are heavy - but not that much.
I really like the idea of introducing trading for items and resources that are not directly related to crafting. Ports are trade nodes, but could become cities too, with a population that needs to be fed, housed, protected, cared for (sickness - yellow fever, malaria, dysentery, etc., etc), and entertained.
So, as a port grows (as its hinterland becomes developed) there develops a need for business to sustain and nurture it.
This could lead to role in the game for developers/owners. From basic resources that are listed already, a need for foodstuffs as you suggest. The more types, the happier the population, the more efficient they are.
Basic housing, shops, taverns, houses of ill repute (perhaps not), coffee houses, arms dealers would be required even at the meanest ports. As a port grows into a city, more cultured housing would be required, raising the requirement for luxury items.
The idea of luxury goods being demanded is a good one. The trade in these would be quite profitable.
These are ideas that would have a profound effect on the game. Is it a direction that people want to go? I hope so, but it seems to be developing into a battle game, which shouldn't be surprising given it's name. I, for one, am more interested in the trading side of things.