I am a long running EVE Online player myself and believe that the loss of your hull and the cargo you carry is critical in making sure the economy is managed properly. If I spend several hours/days at sea killing, looting and hoarding riches it should be a risk for me to enter a port where I could be gangked by pirates.
With this being said I also believe there should be a salvage classed ability present in the game where players can find lets say powder barrels, rum barrels, or crates floating on the water where a ship sank, cast some nets and depending on skill salvage some of the wreck. Salvaging and exploration are huge parts of PVP driven games. The ability to pass intelligence on to others with the effect of changing the player comfort level is needed to keep the game dynamic and engaged.
For instance, lets say that you know a clan is running a major campaign somewhere along the coast of the Texas Federation and they are receiving supplies from the Bahamas to support their efforts. You do some basic sailing with a fleet and discover they aren't using a normal trade route to get supplies there. Hiring an explorer to discover this route and help to setup an ambush to interrupt the supply chain would add a level of realism to the game that exists in a few others. In Texas you stop receiving supplies because of a compromised trade and hauling route, now perhaps someone you called a friend quickly becomes someone easy to take over for their existing supplies and resources. This will help with an evolution process that will prevent the game from becoming stagnant.
Commodities are a question for me as well. There are many resources needed for crafting, and feeding the troops. I have not tasted the waters of the open world yet but I am hoping that resources are more than just wood, metal, stone, etc.... Many of the most valuable things moved on ships back then were Rum, Salt, Sugar, and Livestock. I am certain that a game publicly sold on Steam will not trade in slaves, but that was a highly sought out commodity as well in the early America's, will these be replaced with prisoners?
Food for thought,
Red