Excessive CO2 causes blackouts, IIRC. The only snag is that you need to modify the scrubbers to prevent them from clearing it.
You actually need to modify the Air Alarm in like two ways, I think. First, you have to disable CO2 scrubbing, then you have to turn the maximum allowance for CO2 before it triggers an alarm way up so that the emergency shutters don't cordon off the area. Alternatively, disable alarm entirely, but that'll call more attention to it. It takes more time, but is probably extremely effective at silent murder. I don't know if they get the "can't breath no O2" HUD symbol, though. That might alert some people.
Also, pretty much infeasible if you have an atmos tech who pays attention to atmospherics. Even worse if he's the kind of atmos tech that wears their hardsuit and a large oxygen tank for 4 hours straight.
Oh, yeah, I keep forgetting that you can change those settings. CO2 murder is best in easy to contain areas so they don't find a crack to slip out of.
Dealing with suspiciously well-prepared atmos techs is surprisingly easy, at least as an AI. If you're not afraid of being loud, syphon rooms they'll walk into at some point. If their magboots are off, they get blown in and take some damage. Then they turn on their boots and move slowly enough to get caught in a crushing door.
But, yeah, AIs have a lot of tools at their disposal, most of them louder than a stealthy AI would like. Flooding the station with nitrous/CO2/plasma, syphoning rooms for airflow booby traps, electrified doors, detonating the supermatter, holodeck carp, bolting open external airlocks, killing people in genetics machines under the guise of "backing up their SEs," pumping people in sleepers full of soporifics, disabling the cryogenics freezer... So many delicious options to kill people if they're at the right spot at the right time.