Regarding Chlorine and other toxic gasses I can only comment on my experiences from my Chemistry and O-Chem lab classes I took as an undergrad. Having breathed said toxic gasses (either through my own experiments and accidents, or turning head first into someone elses) unless you've got a hood or other way to suck the contaminated air out it will persist. While the source can be neutralized to stop more gas from being created you still have to deal with what's made it out into the main compartments.
One suggestion (albeit kind of a cruel one) would be to use the crew as human air scrubbers with their escape gear (since sub-wide air scrubbers didn't exist till many years later) and in-game loose hp over time (for those in the affected compartments) - pretty much would mean that the repair crew are the ones that take the damage. Since compartments could still be sealed, if the aft batteries were damaged by the forward intact, crewmen in bad shape could go to the stern quarters to recooperate and regain hp (would actually make having an officer with a medic qualification beneficial) until they're ready to go back to repair work. Chlorine gas is the worst, since it's short 1 electron from being balanced any chance it gets to bind with something it will - which on a sub was really only one thing - a persons lungs (or the carbon in the respirators if they were wearing one); otherwise the gas will linger around as a snow white looking cloud until something is done about it.
One thing I was going to ask about specifically, though this thread answers it is that the amount of current crew doesn't reduce CO2 production. I rarely have a full complement on my sub, usually at least 3-5 (somtimes more) people less than the max allowed on the sub. Even if the sub never takes any damage, the crew would use up less O2 simply with there being less being consumed. While you can't increase the amount of air contained in the sub, with less people consuming it CO2 will be produced at a slower rate regardless, you should be able to stay submerged longer with a crew of 40 than a crew of 51 on the same kind of boat.
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