I would certainly go with more filtering if that is wanted to get the water clean looking. The possible downsides are that you may find a little too much flow so that plants are blown down or something that you don't like but that would be secondary concern for me. There MIGHT be a small increase in lost CO2 but that wouldbe my number three concern.
I want clean, good looking water first, good looking plants second andmthen worry about losing a little more CO2.
Reasons? I can do something if the flow is wrong and I can afford more CO2 but I can't stand bad looking water.