I don't think you need to worry at all about the drop in pH when you add CO2, it is just changing the carbonate ~ CO2 (H2CO3) equilibrium, not the water chemistry.I assume that if you have good plant growth then the plants will absorb the NH3 and NO2 during the day at low ph and during the night when you stop the co2 the ph will begin to rise again and the bacteria will start performing their function again.
I wouldn't either, a large plant mass trumps nearly all the other biological filtration options., what ever the question is "plants" or "more plants" is nearly always the answer.f you have a large plant mass, i would never worrie about amonium or nitrite,