Yes, you can certainly counteract the dark cycle reactions's (plant respiration) production of CO2 with an airstone on a timer, but remember that you still want to maintain a CO2 level of about 25-30ppm. It sounds like you've got a pretty awesome system (being an instrumental analyst, I'm incredibly jealous) so I'm sure that you can set it up so that the airstone degasses excess CO2 if it rises above 30ppm and stops degassing when CO2 levels fall back down.
If the plants aren't pearling it's a sign that your water is less than supersaturated with O2, either a sign that CO2/lighting is low, which isn't likely a problem, or that your plants are struggling due to a nutrient deficiency. You describe what could be a K deficiency: http://www.csd.net/~cgadd/aqua/art_plant_nutrient.htm
You should be dosing K already since you get so much NO3 from your tap, sounds like you need to increase the dose or frequency of the dose.
If the plants aren't pearling it's a sign that your water is less than supersaturated with O2, either a sign that CO2/lighting is low, which isn't likely a problem, or that your plants are struggling due to a nutrient deficiency. You describe what could be a K deficiency: http://www.csd.net/~cgadd/aqua/art_plant_nutrient.htm
You should be dosing K already since you get so much NO3 from your tap, sounds like you need to increase the dose or frequency of the dose.