Ownership of a port over a non-controlled planet seems to give full smuggling credit for any and all shipments that go to the port.
I managed to take over the port over an empire planet (not independent). Subsequently, they offered a "smuggle resources to X" mission. I noticed that any (mine or independent) freighter docking at the port gives credit for anything delivered to the planet - so I get the smuggling bonus for my own ships as well as any independent (or other faction I suspect) freighter that delivers.
Furthermore, there seems to be an issue with the port-planet shared resources. The port has a listed cargo capacity of 2100, but inspecting the port cargo reveals tens of thousands of resources. This leads me to expect that I'm in the situation of being able to use the planet resources for construction - free of charge, even though I've sold them much of what they have (via port-planet shared cargo).
Warning - if this gets fixed by breaking the port-planet link, then freighter behaviour also needs to be modified, so that smugglers (all freighters?) target the planet instead of the port. Alternatively, a kludge of a work-around might be such that any resources "sold" to the planet by the port should also need to be "bought" back.
Note - it might be worth testing this regarding independent planets. If the code for ports over planets is shared for all situations, the a port over an independent planet should lead to the same situation.
This might not be a bug. It might be rewarding a player for being (absurdly in my case) aggressive in stomping on emerging empires before they can "flower".
“That which can be asserted without evidence, can be dismissed without evidence.” ― Christopher Hitchens