Yes, you are correct about fish and plants both releasing CO2 at night and that there is a possibility of a lack of oxygen in the tank......but only in a heavily stocked tank. I have about 25 - 30ppm CO2 running all day in my 55 gallon, and I don't turn it off at night. I check on the fish in the morning for a while after fiddling with CO2 regulator/needle valve, and have seen no problems or stress in the mornings. I do have a decent amount of surface movement, although not agitated surface. A slight ripple is the most that happens, even when the water gets real low. I have a LOW fish population, by any standards, and PLENTY of plants. I actually have at least 90% of the substrate covered (no joke), since I'm trying to get my tank established and stop algae from taking over.
As far as all that CO2 driving out the oxygen, this isn't what's actually happening. While O2 being pumped into the water does gass off CO2, the reverse doesn't happen. The fish/plants utilizing O2 without the plants reproducing more O2 is why the fish run low on oxygen. This is why most credible aquarium plant setup guides state to lightly or moderately stock the tank for best results. It also has a big factor with algae growth.
I'm a firm believer that if you are not using a CO2 controller, then you should leave your CO2 running all night. If you are having problems in the morning, I'd add an airstone and small air pump and set it on a timer to come on at night. Better yet, I might even try having it run for a period of time, then turn off for an hour, then run, turn off, etc. I'd fiddle until I got things balanced. I'd also cut the air pump off about an hour ( or maybe 1/2 hour) before the lights come on to build up some CO2 for early photosynthesis.