creating more surface agitation does offgas co2 from the water column, but not by very much. Surface agitation also does increase the O2 levels in the water considerably, allowing the fish to cope with much higher levels of co2, (in my tank almost double). So long as your not adding co2 at night, and you have a good ripple on the water surface, your problems are going to be minimal provided your dialing in the co2 amounts with your drop checker properly.

Id suggest that if your still having troubles and doing both of those things, that your co2 is way higher than you think it is... and therefore, excessive.