CO2 is for the plants, not pH control. I turn it off at night. If you have a pump to feed the CO2 gas into the tank, simply plug it into the light timer.
Amano says the Japanese think adding CO2 at night is Taboo. Interesting comment.
I don't think it matter too much one way or another.
I've had so called sensitive fish(Altums/Discus) in both set ups, no difference.
I've always had my systems set up in this manner at home.
Clears off the pump to prevent clogging, prevents any slow build up to toxic levels of CO2 if I'm not paying attention since it has 12hrs of down time very 24hrs.
The hoopla over pH swings and preventing this by leaving it on all night is really a BIG myth. Many FW systems go through large daily fluxes in the pH values. Drastic sudden changes in poorly buffered water can cause issues, but not in the ranges of KH's we use generally.
Regards,
Tom Barr