All of that is true but
You can raid to induce shortages
Raiding at least requires interacting with other mechanics, specifically having enough marines on hand and ships with crew capacity which cost upkeep, having to wait time before you can dock and trade again at the raided station, and especially in the case of pirates and Luddic Path planets, worrying about decivilization due to low stability, hitting Chalcedon even once typically sends it to 2 stability. I'm fine with raiding producing higher profits than natural trading alone would produce, since it has a higher investment and more expenses/time/risk of destroying the planet associated with it.
The total profit is so high it really obviates a lot of the other content. I might “only” average 300k month doing it over the course of a game but that would include me doing a lot of other stuff.
When I need money I make a run of heavy weapons to Chalcedon and make a cool 500k.
But I don't think you are running heavy weapons to Chalcedon non-stop and making 5 million profit in 5 minutes or anything like that, right? I believe there's some kind of ceiling based on time elapsed for the background supply/demand calculations updating.
All I'm saying is if you want to reduce profits, reduce the amount of deficit induced by a single minus red supply icon on the smaller or less developed worlds. If Chalcedon capped out a 300 units deficit instead of 600, and 900 credits per unit instead 1200 credits, then your profit of 500k drops to like 150-200k. No need for credit caps that impact other profit making methods, like exploration runs and selling blueprints or colony booster items, or forcing you to be friendly the Hegemony and going to Chico or the size 7s as the only sensible places to sell.
The question comes down to, how much profit should one be able to make on the lower risk campaign layer tasks? As it is right now, the main story line contact hands you between 60-90k for each mission shuttling between core worlds in a single hound with no credits invested in cargo (takes all of 30-60 seconds to accomplish), and commission pay between 25-95k per month no matter what you do (and if you're in the deep black exploring, the potential extra hostile factions makes almost no difference). If deficit trading is over performing, it's probably no more than a factor of 2. I'd certainly be wary of creating a new mechanic that caps small planet purchasing power from the player to 100,000 credits for example, which would make selling an exploration haul a pain. At that level, trading with the planet is about as profitable as an exploration or shuttle mission. And if it's capped at 500k, that doesn't preclude the drop off 1000 drugs for 500k which is pretty close to profit now, and still potentially makes some large hauls with good survey data a pain to sell.
In answering that question, you need to keep in mind the game is intended to be played on iron man, and in a mid-game fleet wipe situation, you want the player to get back up on their feet relatively quickly. To be honest, these days story points and skill points are more of a power limiter than credits (which is why I believe Alex was going to make ships with s-mods that get destroyed and not recovered provide bonus XP, as well as tweaking the bonus XP earning rate, at least the last time I read about it), so relatively easy non-combat credits may be intentional. Late game colonies profits (or even mid-game colonies in cryosleeper systems) make me think that is true.
But, black market trades don't have that effect.
They kind of do, although the sell interface doesn't show it. In a vanilla game, if I go to Chaledon, and look at the deficit and price per unit before selling 1000 supplies while in deficit, and after, the deficit number has gone down by 1000, and the amount they are willing to pay also goes down per unit. If I sell them 20,000 units as an extreme example, the sell price per unit drops to something like 50 credits per unit, well past excess price stages and certainly not making a net profit. I admit planet interface still shows red supply icons, but the deficit/pay significantly higher prices condition did disappear. So the mechanism limiting profits is definitely there. The next month when the colony information updates, it still wasn't in a deficit state (i.e. really high sell price) but only at ~80 credits per unit sold, despite having a bunch of red supply icons, so I'm not exactly sure what is going on under the hood. It may just be a graphical thing (possibly intentional, if you're doing black market trades, how does the colony know how many supplies are actually available if no one is counting?), but I'm not sure.