I usually get a big boost to my resources after a pogrom, even with aircar, it's potentially worth it. I don't do a capture only run, though I do like to capture, sometimes it's too risky, sometimes I they do that civilian in an arcade shooter thing and walk in the wrong place with the wrong twitchy gunner, sometimes they just piss me off. I've not had too much trouble with money, except for when I forgot to set my runts to actually work.
Might have mistaken your situation with someone else who avoids civilians like the plague, they have the same negative score for capture as killing, but are pretty good subjects for research and/or ransoming.
I do play on the second difficulty, and am not very far into the game, I've avoided fishy missions so far and mansion missions are just a little further than I've gotten before an update shows up. Monster hunts are fun, especially with light auto weapons, haven't gotten lucky enough to meet a chupacapra.
On missions, what you get and what you find is random, I believe it's set at the beginning of the month. You get an unlucky group of missions and you're going to be waiting.
Honestly, none of my runs have really been very similar to each other, the mod is vast enough that you run into strange things at times.
Also, as I understand the premise, the game tells you that you're a pirate, have fun
