I guess it would all depend on how the skies were darkened in the first place. The process of darkening the sky was discussed in one of the Animatrix films but it was never said what was used to darken the sky. All we saw were planes streaking through the sky with a dark substance coming from the rear. I can't think of a chemical that would be as permanent as that. Hopefully, at least not in my lifetime, there will never be a need to scorch the sky because there is another life form on the planet that needs solar energy more than we do. The ozone problem is the closest one of that nature that we have today.
It is true that the lack of sustained light would cause a severe cut in oxygen but there are some subterranean plants that do produce oxygen. The process can also be synthesized using lamps so at the very least Zion would be able to sustain itself. A very interesting question though... Got me thinking,