UPDATE:
After I came back to the game, several POIs have spawned on the surface of the target body, that weren't there before when I did the surface scan.
Two of the POIs were "Irregular markers", which are the aforementioned cargo stashes guarded by skimmers. Both belonged to the target faction, and all skimmers counted as mission targets.
This would seem to be the intended way of completing this kind of mission.
The issue was the POIs not spawning at first. Only after re-log. Also terrible information communication form FDev, as it was not clear that ANY skimmer from this faction, not only the one from target settlement count towards the mission.
Thank you all for a very productive discussion and for your input.