So here's my take on all of this talk:
Does it thematically fit that you produce metric shittons of grog to sell on market to fund your crew and operations? Probably not.
Does it work well as a game mechanic? Hell, YES.
While there's a lot of things that have changed from vanilla to this mod, almost all of which is super in depth and wonderful, when the game requires you to manage certain resources to keep playing, making that more complicated may not be the better solution. Even if it breaks the immersion a little. So while producing X-grog to offset your maintenance costs is a little not-so-pirate-y, it makes sense from a purely gameplay perspective. If you have an alternative that doesn't bog you down in TONS of micromanagement, that might elicit a better response and I'd be all ears myself. But in game with SO much to do already, making something that works as it should more complicated for little to no reason is probably not constructive.
That being said, I agree about making looting ships would make it feel more thematically fitting. BUT, I also understand Dixione's argument about adding purely "sell only" items is actually just going to clutter things up more. While it would be more fitting of the feel of the mod, it isn't entirely necessary. Would it be cool and fun and give incentive to attack that large cruiser that could be carrying tons of cargo but has units up the wazoo? Sure. But does it unbalance things? That's debatable, and I'm probably going to end up siding with the dev on this one, regardless of what I'd "like to see".
Lastly, and this is kind of not important since it's been stated that coding the market thing would be hard and I can't see too many people willingly taking on that headache, but I'm really against that idea. Unless you'd like to throw in different items to manufacture that take no materials, you're just shooting yourself in the foot. This comes back to the realism/game balance argument above. It makes much more "sense", but needlessly drags you down into managing things that don't add any major value to the game.
Just my 2 cents.