You mention seeing bubbles on your plants and say it is from the micro bubbles of CO2. It may however be something called pearling, which is oxygen being produced by your plants, normally indicating a happily photosynthesizing group of plants. Pearling shows up as bubbles adhering to the leaves and sometimes as a continuous string of small bubbles from a leaf, especially from a damaged portion of a leaf. Pearling will start after the lights have been on for a while and most folks consider it to be a desirable indication that they are supplying sufficient light and CO2 to their plants.
I agree that you are not likely going to gas your livestock with a DIY set up and it won't hurt to leave it on 24/7.
Your timed air stone is a good idea (I run one in my tank too) but you are not really adding oxygen to the water with it and oxygen dosen't cancel out CO2. What your air stone does is help promote the off gassing of CO2 from the water by increasing the surface agitation and by flushing out any CO2 held at the water surface, especially in a lidded tank. It is not that your plants mind the CO2 at night it is just that they don't need it. Having a higher % of dissolved CO2 in your water dosen't necessarily mean you have a lower % of oxygen, it all depends on the partial pressures of the gasses in the air that is in contact with the water. You can have a higher than normal CO2 & oxygen at the expense of the dissolved nitrogen content.
I would suggest your air stone start at the same time your lights turn off and then stop about 1 or 2 hours before they turn on.