Thanks! I ran the same question in reef forums and here were the answers I received. So maybe we do have some things to learn from across the other side of the shore... Below are two of the more informative responses were (as relates to marine, though similar in underlying biology). End result is that I've decided to start with putting a drop or two of white vinegar in my tank daily, adding the carbon back in, and not worrying about my UV sterilizer circumventing denitrification -
A. I expect that some portion of dosed organic carbon does indeed act to drive denitrification. What portion probably depends on what is dosed and a hundred other properties of the tank system,.
B. The organic molecules can end up as CO2, primarily, or can get incorporated into bacteria tissues.
C. GAC won't remove the usual sources of dosed carbon, such as vinegar or vodka.
D. UV won't do much. A lot of ozone treatment might oxidize some, but not much. The molecules we dose are fairly resistant to ozone.
E. Couldn't say what media is best. Live rock and sand might be more than enough when dosing organic carbon.
Many denitrifying filters utilize some form of organic carbon. Older Aquamedic denitrators, coil denitrators, and the newer Aquaripure denitrators all use some form of organic carbon that is readily mineralized.
So, you've mostly answered your own question, actually:
A). Yes, it is, as you've said, completely dependent upon availability. Inorganic carbon is also used by some bacteria, but that usually isn't an issue in seawater up to an extent.
B.) The carbon is oxidized in the process into CO2
C). In many cases, that probably isn't necessary. In the aquarium, there are usually plenty of sources at the substrate level. In seawater, it is best to have activated carbon to help lower concentrations of organic carbon, considering that many organisms (corals included) make lots of it.
D). Some work has been done to show that ozone use can potentially enhance it by breaking down molecules that are normally much more difficult to metabolize. I think it is somewhat plausible that the same may be true for UV sterilization. There are some papers available on the subject, but I haven't looked into them completely to know that this is the case for sure.
Edit: skipped E, lol. To be honest, I'm not entirely sure on that one, either. I would assume media that have a higher internal surface area would be best. That would serve, up to a certain point, to not only provide as many settling points as possible, but to start limiting oxygen as well. As long as you provide the appropriate external conditions, any porous/higher surface area medium can be used, AFAIK