I think the black market should only be accessible with the transponder off (or with the Free Port modifier, maybe). I also think that planets that have had significant player black market activity should spawn more patrols fast - starting just a few days after the smuggling event and lasting for months - scaled in power or number of fleets relative to the amount of money involved. Above a certain threshold they should also spawn bounty hunters looking for the player, that can be bribed to go away (possibly with SP + bonus XP) for an amount related to the money involved.
Reasons:
Smuggling as a money making source is a major problem in terms of gameplay: it is profitable and risk free, so naturally people do it. Once the player has identified a market and source, its just click and hold down shift to make a few millions running the route: frankly a boring experience.
Requiring the transponder off immediately makes grinding money more difficult, but more importantly ties smuggling more firmly into already existing gameplay mechanics that are often overlooked: sensors, stealth, misdirection, and the actual details of solar systems/their terrain! Sneaking into markets is very doable even without a stealth fleet in a number of heavily patrolled big worlds, but requires effort and skill, which should be rewarded.
Smaller markets that lack (and possibly those with the Free Port modifier) regular patrols are an opportunity for the player to get easy black market access. They can sell off their exploration loot without tariffs, get better weapon/ship access, and do smuggling there. It gives a difference in player gameplay experience between the big stable worlds and the small, wild west planets.
Spawning the commerce patrols after black market activity is a measure to stop player from abusing those easy markets in the exact ways they are right now, with regular smuggling runs. Once the player has done their dropoff of heavy armaments at the luddic path base planet for a single massive payday, they are going to need to dodge patrols to do it again. This forms a soft "cooldown" on smuggling, only one that can still be gotten around with player skill and a stealth focused fleet.
The bounty hunters are the last step that funnels the player towards combat: they are going to have to either give up parts of their profits to bribe the fleets, take along combat ships and fight, or get really good at dodging fleets. Any of those are much more engaging than current smuggling gameplay.
One critical thing though: bounty fleets should never spawn on the "first offense" at a planet, with an appropriate cooldown scaled to the amount of money involved, and it should be clearly signposted when the amount of smuggling is high enough to attract one. The reason for this is that selling off exploration loot at un-patrolled markets should not be penalized: it wasn't gotten through grinding, but through exploration. Neither should selling off the loot gotten from opportunistically hitting a trade convoy: again that wasn't gotten through grinding, but through combat and required at least some combat ships.
