I now believe I was affected by some bug that prevented reputation loss from bounty kills. Some time after I started this thread, the things I described in the OP changed and reputation started behaving like everyone else has always been describing it. Call me paranoid, but FD may have seen this thread and fixed the bug throwing me into what I would like to call from now on Bounty Hunter Hell. I can really feel for you all now.
There is the new community goal in tanmark, to hunt bounties. It is utterly frustrating having to check dozens of ships in order to find one ship that finally is of the criminal faction Tanmark Posse, and doesn't belong to a local corporation or, worse yet, the one that belongs to the Empire. I really wanted to do this community goal and participate all the way until the end. But after 3 hours I am already fed up. I lose probably three quarters of all bounties because the ships are under that magical protection of their factions. The only alternative is to see my reputation with all but the local authority faction ruined, and my Empire reputation wrecked at the same time.
(It's also odd, though working just as described by the devs, that wanted ships which belong to the system authority faction, do not yield a reputation loss because "it is their faction that issued the bounty". Such a weird, 4th wall breaking game mechanic.)
This really needs to stop, it can't go on like this. Either make it so that any legal faction (i.e. not "unfettered") accepts the law and you don't lose rep with them for taking out the bad apples out of their ranks (why do they all even employ actual "give me your cargo or I kill you" pirates in such large numbers?). Or, at the very least, if FD is adamant that this ought to stay this way (why?), shows us clean and clearly in the target UI (not the contacts panel, too cumbersome) whether at least part of the bounty has been issued by their own faction, in other words, whether we are actually allowed to kill the ship and it is not just a reputation killer trap.
P.S.:
And i prefer the Elite system, if it ever was in place - kill a faction member - they hate you, even though they were wanted. You know, loyalty in space and all.. So i have to choose carefully, who to kill using the KWS, not blow up everything that flies mindlessly.
It would be fine if those were the exception, not the norm. But currently you have to heavily cherry-pick the rare few ships that belong to actual criminal organizations, all the time. It nice that in 1.2 we will see the target's faction in the target panel, at least, but it doesn't solve the underlying issue.
Also, it is absolutely strange, quite disturbing indeed, to see an innocent freighter attacked by a pirate and being unable to help because the pirate belongs to a totally legit company which doesn't have a clue what their employees do in their free time. Like, I am there with the guns and everything and watch the freighter die because I am the one being punished if I dare to help. So much for that.