It would be very rare for anyone using DIY CO2 to be getting such a high CO2 concentration in the water that they need to reduce it at night. If you have around 10-20 ppm of CO2, which is very good for DIY CO2, the concentration will not increase enough at night to justify doing anything to reduce it. The only safe way to "shut off" a DIY CO2 system like that is to disconnect it or remove it from the tank, which would be a very tiresome thing to do every night. Turning off an airstone at night won't do any harm and will reduce the CO2 concentration a little, but it shouldn't be necessary.
Whether you have CO2 or not, it is a good idea to have the tank water surface covered with ripples to help maintain more dissolved oxygen in the water. Higher oxygen content will help the fish live with the CO2 you add, and will help the fish and plants even if you don't add CO2.