The main benefit I've seen to going lethal is that armor-piercing stun weapons are really rare, while you can unlock armor-piercing swords pretty fast (plus grenades, which IIRC beat armor but not shields).
Although there's a certain fun in flinging armored enemies out of your way with the concussion hammer - shooting or bashing them stuns them for at least half a second. That includes hitting them with a wrench, then throwing the wrench after them as you scurry off, such that it hits them again as they recover. Then you tele-retrieve the wrench, leaving them confused...
They won't actually sound the alarm for being hit by something! They have to CLEARLY see an intruder, see a body, or hear a gunshot/explosion. maybe you were just a space bat, not worth filing a report... This is also why stealth devices are really great, and slipstreams are so amazing that they hardly ever spawn on daily challenges (look out for jammer doors though).
Going bloodless mostly just nets you those contracts, though it's nice not to worry about shooting fuel tanks or my abduction target by accident. In return you give up some tools. Of course I still use those tools plenty in the daily challenges and defector missions, which are all about challenging one's preferred playstyle~
furthermore, defenders delenda est They're not
faaaair! Crashing them should disable their ability, or at least subverting! Stop challenging my preferred playstyle dammit
They make me use more glitching, but they're so hard to isolate from their packs... Avoiding is often easier than neutralizing, whereas every other contractor gets a hammer. Particularly trackers, but even uncrashed predators when I have a long enough hallway~
Bouncing hammers into trackers has got to be one of my favorite things in the game, hehe. They went from requiring equipment to mostly harmless when I figured that out. (Also, they'll try to shoot through the crew like everyone else, and that's soooo annoying on bloodless/pacifist missions. Can save your life though.)