Since random sector generation is now a thing, I'd assume there will be random markets... How would economy system go with it?
I'm not sure why you'd assume that
In my mind this isn't directly related to procedural generation of more star systems. Not to say there won't be some dynamic markets, but the economy is quite capable of dealing with that; not sure I understand that question.
Regarding the idea of having your surveys be interrupted by hostiles: SPAZ 2 had a nice way of dealing with this, performing an action (harvesting) accelerated time around you.
Right - Mount & Blade also did something like this - rather, pretty much exactly this - with waiting/looting villages/etc. For Starsector, I don't think speeding up the game beyond what pressing shift already does is viable, performance-wise. I'm also not exactly decided on whether this kind of approach is good in general. If it's something that happens often, it could get annoying, fast-time or not.
For example, say the game design goal is "your action can be interrupted by hostiles" - but, really, is it that, or is it more that you want the action to possibly result in running into hostiles? If it's the latter, which I think it more often is, or is at least a good substitute for the former, performing the action could just trigger nearby hostiles to go look for you, no waiting required.
Still thinking this through, though, so might change my mind.