Checkin wich state it is settlement you gonna target is crucial. You need be in system personally, and then map will show all current BGS states. Some BGS states means empty bases, so as others said, then worth to take while to learn and know wich one is wich. Atleast those ones wich means empty bases.
But yea, game can sometimes give such a mission, where tells: "GO TO X SYSTEM, KILL 18 X FRACTION MEMBERS, while currently there might be no active settlements at all, due of BGS, its more likely to happen on systems where is only a few settlements, and less on those systems, where is tons of it. Still, there is also other ways if that fails.
But again, as already mentioned, if that happens, POI are viable too, as those will spawn local criminals, and it will be counted as well. In fact, that might be preferred way to doing this type of missions for many, well... just for weapon schematics from any irregular markers that have threat level.
So if there BGS mess, check planets for POI, find just one. You wanna this: Ilregular Marker (threat 1-3) and any variant of this is good. There two variants of this, one with 2 containers + crashed skimmer (only place to get settlement defence plans) and other with 3 contatiners. But sometimes no NPC spawns. It might spawn with group or empty where npcs came from ships afta few mins. Exit to windows to log back, will reset POI, all things and npcs too.. bring tons of e-breaches too, you need it to open yellow boxes with password.
If there is no any POI, jump few systems and go back, POI might be re-rolled, and repeat until find good one.
So while it might be more hassle to look for POI instead of finding right settlement, it certainly can be completed either way.
... and local POIs had in my case nice views 
