1. Since you are a pirate and are looting freighters, i think that indeed of always findin weapons, ammo and jewerly each once in a while in addition to spare ship parts, most trader vessels should contain actual cargo. For example, bounty should consist of several types of "cargo crates" which basicly hold commercial wares that have only one purpose: fence them.
Im think there should be a few types of cargo crates, called "Merchandise Crate" or "Entertainment Cratess". Depending on the size of the vessel, you can find like 5 to 30 of these cargo crates and they should be the main way to receive "income". This would fit with the whole "Pirates" and "Booty" theme a whole lot better than manufacting a gazillion metric cubes of grog.
Secondly, i dont know if its within the scope of the game engine or can be added as a code mode, but i think it would be very, very nice if the fence market would actually appreciate shortages and overstockages with decreased or appreciated prices. Coming back to the gazillion barrels of grog, even a very simple variable and loop should perhaps be able to decrease the sell value of grog over the course of a game, while increasign the price for more rare commodies.
Im sure there are more good suggestions, but i cant think of any right now.