Depends on the amount of co2 you are injecting. For example, a lot of DIY doesnt have a "off switch" so it runs 24/7, but it is usually only putting a small amount of co2 compared to pressurized systems like your paintball (depending).
When the lights (photo period) are off, the plants are no longer photosythesizing, so they aren't using up the co2. So if the co2 is still being injected at night and nothing is using it, the levels of co2 can build up to dangerous levels and potentially kill all the livestock. It's also kind of a waste since some of the co2 being injected will be off gassed (happens all the time, but usually just the hours co2 is needed).
So it depends how much you are injecting if itis safe enough for fish to live through the night or not. UNLESS, you provide more surface agitation at night. What that really does is off gas the co2 so levels dont build up to dangerous levels, which again wastes co2.