Hi,
You are right if there is more CO2 in the water than the equilibrium value with the atmosphere it will be lost, but if the water is CO2 depleted it will gain CO2 from the atmosphere until levels reach equilibrium (and vice versa).
Trickle filters work by having a large film of water which can exchange gases (N2, CO2 and O2) with the atmosphere.
You can think about like the diffusion of a coloured dye (say red food dye) through a permeable membrane (cotton handkerchief) into a bowl of water. The dye will diffuse out through the handkerchief until the water is uniformly pink, rapidly at first, but more slowly until an equilibrium level of pinkness on both sides of the membrane is reached. The rate of colour change will depend upon the permeability of the membrane (either how big the holes are and/or how thick the membrane is) and the eventual pinkness on how large a volume of water the bowl holds. If the volume of the bowl is large the final level of pinkness will be very low, and if it is very large it may well be undetectable.
In this case CO2 in the tank water is your dye, and the thin film of water (in the trickle filter) the membrane and the air surrounding your trickle filter the bowl. Assuming your sump is open to the atmosphere the CO2 will rapidly disperse into the surrounding air (so basically an infinitely big bowl) and be lost, the differential in CO2 concentration will remain large and CO2 will be out gassed from the water until it equilibriates with the atmospheric level. If, as Clive suggests, the filter in enclosed, the "bowl" will be much smaller and the differential between the levels of CO2 in the water and the air in the bowl much smaller, meaning diffusion will be much slower and more CO2 will remain in the water.
The effect of turbulence is to increase the area of water in contact with the air, you can just think of it as it makes it a thinner film. It is only if the CO2 level in the air is in equilibrium with water that it doesn't make any difference whether the water is turbulent or still.
Hope that helps.
cheers Darrel