Thank you for the detailed answer.
These seem to have had literally nothing. So, if they are always supposed to have at least some conventional industry and troops, I may have encountered a bug. (I haven't read all the latest bug reports and fixes. Plus, they may have been generated in a previous 1.9.x version, I'll have to check the log.) I'll go through my backups with more time. But the problem presumably occurs at the moment they are generated. And that would be impossible/very hard to reproduce.
I had actually parked a small jump-capable diplo-ship with a large "Shoot me, I am here" sign (activated transponder for all) in orbit after making sure that there were no ships, no planetary forces, no shipyards, only a large EM signature, and a smaller thermal one. "Attempting" communication (it remains there after conquest), no further messages I can remember seeing. After roughly two years and nothing else to do with them, they were annexed. No combat, immediate capitulation and handover after bringing enough troops. And they have 0 anything, not even CI.
But it doesn't break my universe in any way. And they do have useful environmental tolerances, so they will be turned into a valuable member world. Non-violent victorious war: My next election is as good as wrapped up. All I have to do is find a way to silence the Federalists and Nationalists who run around on the streets in front of my office shouting "inhuman warmongering", "reckless entanglement in xenoaffairs" and other such nonsense...