Tips for killing enemy crew without use of boarding parties
I'm a fan of capturing enemy ships intact if possible, due to the greater rewards involved. With a teleporter, a couple of Mantis "spare" crewmates and an S. Bomb, this is very effective.
However, I wonder if there are any remotely effective techniques for destroying the crew while leaving the ship intact, if you don't have a teleporter? (Or equivalently, if you have one but no feasible boarding party.)
I've managed to asphyxiate the crew once before, but in general I find this to be very difficult - it's hard to keep the O2 system down without causing extra damage to the ship's hull. And since it's a waiting game for the O2 levels to drop, it's likely necessary to disable the enemy weapons/drone systems too, causing further "collateral damage" to the hull.
Could ion weapons be a feasible way to do this, or would it take two or more (i.e. an unlikely number to find) to pull this off?
Are there any other approaches that would work - fire, for example? Has anyone had success with using fire bombs/beams to specifically target the crew? Did you have problems with rampant fire causing damage to systems and thus destroying the hull?
In any non-boarding case, I recognise that you almost certainly need to know where the enemy crew is, so I'm assuming that upgraded sensors, or a Slug crewmember, is a prerequisite.
Breach bombs damage systems and crew, and cause cracks, but don't hurt hulls. Alternate bombing the medical bay and the O2 generator. Put priority on whichever one the crew is trying to repair. Eventually they'll have so little health they won't try to repair things, and you can just wait. If the ship doesn't have a medical bay it's even easier - just bomb the O2 generator until they stop trying to repair it.
If you're taking this tack, it helps to upgrade your own shields (and maybe have a defense drone) so you can sit and wait them out without having to waste missiles bombing their weapons as well.
Ion weapons can help, but it's hard to get enough of them to punch through 3-4 shields reliably, while you are still getting shot at. If you have them, great, but don't prioritize them.
You are correct about sensors. Don't even bother trying to kill crew without damaging the ship until you have the first sensor upgrade or a slug crew member.
Anti-bio Beams are incredibly good at killing enemy crew, if you can find one. They need the target's shields to be completely down, but will kill most races in 2 hits and have enough range to hit 2 or more enemies most of the time. Arguably the fastest, safest and cheapest way to kill enemy crew. I used anti-bio beams and burst laser 2 throughout the game (on easy), only switching to other weapons to deal with the boss and unmanned ships.
The Slug ship is great for this, as you start with Anti-bio Beam, Breach II and Dual Lasers. Use breach II when you need to keep multiple systems suppressed until you find some better rapid fire weapons. Get a Defense drone Mk 1 to protect yourself from enemy missiles and you are golden (just completed a run on easy with this setup - maxed out every possible subsystem, bought a bunch of stuff and still had scrap to spare).
Some ship layouts have a disconnected O2 system. If you can take that out, the enemy crew will be totally unable to repair it.
Fire beams/bombs can also be cheap and effective but you have to be careful - as you mentioned fires can damage systems, leading to hull damage. However, fires spread, and cause severe damage to the crew. Aim for the med bay so they can't heal themselves, and as long as they aren't rockmen they'll eventually burn to death or asphyxiate (fire eats up O2 really fast - speed this up by keeping their O2 system down.)