You not only get more scrap, you get more everything: fuel, missiles, drone parts/schematics, weapons, and crew members. So you get more scrap AND you offset other costs, AND you're more likely to get stuff to sell/install.
In short, take out enemy crews. Period.
If you don't have a teleporter and a Mantis assault team, you can upgrade your scanners and fire on manned systems (usually the cockpit, shields, and weapons). If you get lucky, you can wipe out the crew before you destroy the ship. This is a good idea even if you have an assault team in order to soften them up for boarding.
Also, -Never fire on a system with your boarding party in it. -Never fire on a ship that has a small amount of health left. -Always fire on their medical bays if they have them.
Additionally, -Upgrade your teleporters. If things go badly you may not have 5 more seconds to save an assault team. It makes a difference, trust me.
-Upgrade med-bay. Works great with upgraded teleporters: send in the assault team, do some damage, then pull them out and heal them before the other ship can recover. Repeat as needed. Not the easiest way to take out a ship, but can be helpful in those "tough nut" situations.
Check out www.axemurderingworms.com . And remember kids: Sound isn't music, Books aren't stories, This is not a pipe, and The medium is the message.
That can work (and there's even an in-game achievement for doing so), it can be tough to pull off, since the other crew will (understandably) work feverishly to get their oxygen back online. That means you need to keep attacking it, which means you need to keep damaging their hull. It becomes a race to see which gives out first, the air or their hull. (There's also the problem of their weapons attacking your hull, while all this is going on.)
That said, every once in a while, you'll find a ship with the O2 room completely cut off from the rest of the ship. If you destroy that, that's it. They have no way to reach it, so they can't repair it. Then it's simply a matter of making sure they don't do too much damage to your ship while you wait for the air to run out on theirs.