The problem with unwrenching pipes comes from the change that was made years ago to allow pressurized pipes to be unwrenched safely without a pipe freezer by simply standing on top of them, plus whatever was done to reduce the damage done by unwrenching from the side. Back in the day people learned quickly not to mess with pipes without the freezer.
Wrenching off a pressurized pipe should deal serious damage. Just give atmos techs back a pipe freezing wrench that prevents it.
Botany changes that removed strange plants that produce gas also had a little impact on the importance of vents. Lower frequency of space carp breaking windows also had a little impact.
Negative effects for closed vents/scrubber that wouldn't break immersion (i.e. not buffing CO2 respiration when it's just a 2h shift):
* Scrubber filtering could intake a bit of O2 and N2 along the contaminants, not so much that it creates drafts, and normally will be replenished easily by the vents. You start welding things shut and uncompensated scrubbers here and there start to mess up pressure. This may not be feasible though if performance relies on not having to update many tiles each tick, so maybe they should only suck O2 and N2 when the vents in the room are off or closed and we just pretend they do all the time.
* Fires could release more CO2 than they do now, including some "effect" fires like phlogiston that probably don't release that much, if any.
* Add "noxious" (CO2) and "toxic" (N2O) types to the atmos anomaly, they'd emit gas (which doesn't clear by burning) and spawn an oil / silver slime.
* Running PACMANs should produce almost enough CO2 to saturate the room's scrubbing.
* Scrubber backpressure event could include gas releases. Or it can be a separate event.
* Kitchen machines could release some CO2
* Trays and plots could produce small amounts of O2 and N2O (fertilizer and bacteria do that), and maybe bring back gas production for random mutations.
* CO2 build up at room temp or colder could sporadically cause wet tiles (i.e. as a proxy for water condensation)