The main problem right now comes from the purpose of the 3 markets.
Current implementation:
1. Normal market-
Worst selection of items, heavy markup. Almost always available (non hostile).
2. Military market-
Same markup as previous market ( i think?), better selection of items, access limited heavily by nation relations and commission status.
3. Black market-
Same selection of items as regular market + some, but with lower quantities. No markup. Possible relation penalties/issues.
I really don't think this models the idea of a black market well. ANY play ship can dock in full out transponder mode, ALWAYS knows where the blackmarket is/how to reach them, and then can trade freely among them for minimal penalty. I will always do black market shopping first and then go to the others as needed. I've yet to really notice any penalty for this. Yeah occasionally I get a rep hit or a bad scan, but it's trivial and rare. Mostly it's just obnoxious having to always hit 1 to quickly get through the scan pop up and then listen to the sound effect to see if i got someone cranky.
I've been working on a fairly large post on some economy tweaks to suggest, but part of it touches on markets (although a major portion of it talks about retooling salvage a little). The general gist of it is that so many things in this game are balanced by their "scarcity" and yet aren't really that scarce in practice. A lot of discussions on these boards about weapons/ships boils down to "Why would I use X when I have Y", and often that's supposed to be because X should be harder to acquire, but in reality that's not often the case. Further its SUPER binary where one minute you've got nothing and then a single decent expedition later and you've got boatloads of cash, weaponry, ships, and blueprints.
Suggestions-
1. Normal market-
Consistent and quality selection of items with more feedback.
Some weapons especially should show up here more often. The "upside" of paying the tariff should be reliability. I should be able to know that X planet is where I go to get railguns if i'm willing to straight up pay for it. There could still be limitations depending on relations or ranking (its sort of odd that no matter who you are, with enough cash you can buy anything that makes it to the civilian market).
As for feedback, it would help a lot if it was made more clear to the player why it is I can find mortars everywhere but I sometimes don't see assault chainguns, as if you're totally new it's not even obvious that one is considered better than the other and thus more limited. Someone else already mentioned having to "noah's ark" trade goods, when really you need a better visualization of trade in general to help consolidate the information that you know. When i'm considering using my irl job skills to load trade data into a database to get a better visualization of my trade options I think it shows that there's something lacking.
2. Military market-
Better limitation of some better items to mostly military ONLY. Something as valuable and dangerous as a Gauss Cannon really should be locked down better. Given the current lack of penalties for hitting up the black market you can never pick a side and still just get stuff through black market lotto. I think the raw power stuff should mostly come from salvage/commission, and thus require some sort of investment to find, or accepting that you'll be limited on access.
3. More limitations and interactions with the black market-
Why can a brand new pilot land on any planet and find a fully stocked black market even if they full announced their arrival and are loved or hated by the local authorities/populace?
I know there's a skill rework coming, but just like how a new pilot needs to put points into getting better at piloting/navigation/salvaging, shouldn't your ability to hunt down and interact with the black market and maybe pirates depend at least a little on that? I don't want to totally cut off a players supply to limited things through the black market, but i'd like it to be than a dice roll and a formality.
To start with I think if you come in blaring the black market should be heavily limited in selection and quantity. I game if the authorities know who you are, they could be watching, so you can't get as much access. Might even limit your ability to offload items (since selling is currently unrestricted). Maybe just the basics and in low quantities This then lets you have showing up with transponder off, or even better in "going dark", show you more stuff.
You could go so far as to have it be related to reputation. Either its own metric or maybe make that another reason to be on the pirates/smugglers good side, and to help their presence. A system with a low pirate or smuggling has a difficult to access black market (and thus fewer goods), but if that were to change suddenly its easier (and thus more goods).
4. Tweak trading:
Now that the black market isn't always a thing, you can have "ok" contracts available with more frequency. If you put in the work through skills or in game actions you can get them to be really lucrative with no tariff, or you could see trade contracts for items that can't be sold/bought easily in non illegal means which means you must have a way to get to the black market for that area in order to take them (and they can be more profitable to reward that)
Hopefully something like this would make the black market a "goal" you could work towards and get better at just like exploration (more of a subset of trading i guess). Some playthroughs would never use it, but it gives other options for roleplay as well (exploration/bounty hunter/ military pilot/trader/smuggler)