I have found the missing NPCs issue when it happens to me is not really such. What really happens, at least in my case, is that the killings counter for settlement raid missions does not update quickly enough if you kill several NPCs in too quick succession, i.e. within a matter of 3-4 seconds. The workaround is to check the killing counter goes up after you kill one NPC and before you kill a new one. If you kill a second NPC too fast, before the counter is updated, then the counter will miss the first one.
Overall, I find the settlement gameplay quite a smooth experience, and serious bugs are at this point really rare.
Perhaps that's how it is for you, but I've documented (on video) the exact NPC that vanishes in one settlement at least. It's the same NPC (a guard by the "entrance") every time. I've completed the massacre mission at this specific settlement so many times I know all the NPC locations by heart and this is the only one that is either there (and so the mission can be finished) or is not (and so it cannot and you're left with 20/21 kills). You can actually determine if it's bugged before wasting time by visiting this spot first to check. What I don't know is if this is the same for other setttlements that bug out.
So your bug is a different bug to the one I'm talking about but I've never seen it.
I record everything to video. I'm going to check over my recording to see if this is what happened.
Edit: I just checked my video where I took on a 16 kill mission at
Conteh Hydroponics Market in Groombridge 34 twice in a row. On both occasions it ended up 14/16 and no more targets to kill (and the targets I could kill were the same 14 NPCs).
What you describe doesn't happen. In fact, in one sequence I kill two NPCs quickly, faster than the counter could keep up with, yet it counted both fine. I can upload this sequence to Youtube if anyone wants to see.
So, you're suggesting that settlement game play is fine yet you've highlighted another fringe bug I cannot reproduce as your evidence that it's "smooth"
I think that you perhaps just don't do this mission at these locations like I have and so don't encounter the bug? I'm 100% sure that if you did, you'd encounter the exact same bugs that I have. And they have been in the game for months and should be fixed, in my opinion. Now, anecdotally speaking (as you were), my experience has been smooth just like you.
Until I started taking this mission type.
And that's really my point.