late to the ball game here, but intrigued by the blog post having only just now read it. i like the simplification.
i am tbh not entirely certain of the purpose of shipping capacity, other than insuring there are markets with permanently unsatisfied import requirements; it seems like a stat that only matters if its modified by an event to create temporary shortages?
the topic of how to permanently effect markets and create interesting economic interactions concerned me most; temporary measures obviously wont do when one wants to create a permanent outpost. And you don't really want destroying actual markets to be something the player is engaged in, at least not as a casual thing. The only solution I came up with was feeder outposts and way stations used by the AI. The outposts would function as feeders to another market and not as markets of their own; for example, an asteroid mining facility or a hydrogen fuel-scoop that supplies a nearby market, increasing its production. These would be interactable and destroyable, possibly even the subject of faction missions. Destroying one (or otherwise neutralizing it, like with a hireable spy, skill interaction, or ancient AI virus you found in the boonies) would decrease production and cause a temporary stability hit. Feeder outposts could even be semi-randomized, causing economic variations between gamestarts. NPC Waystations would work similarly, providing connections between markets but able to be sabotaged or destroyed to cause economic chaos.
Now that I think about it, one great advantage of npc waystations would also thematic; the gradual destruction of trade infrastructure and the economic consequences thereby seems central to Starsector lore.