Condensation could accumulate anywhere in your HVAC ductworks. If water is allowed to sit and pool, that moisture promotes bacteria growth, and they poop and fart some pretty smelly chemicals. The only way to get rid of it is to allow your HVAC ducts to air and dry out. Running your A/C produces a lot of condensation, mostly at the evaporator coils buried somewhere under your dash. All that water is both good and bad. It's good, because the constant flow of condensation drainage basically rinses your HVAC plenum where the evaporator coils are, which is typically the lowest point with a drain tube that drips out of your car. It's bad when that drain tube is obstructed or plugged up, so all that condensate has trouble draining out and starts to pool and grow bacteria culture.
First thing is to check your drain tube is flowing well. You should see water dripping out from the bottom of your car, when you are running the A/C. The more humid the area, the more that water flow is. If not, you'll need to clean the drain tube. Get with a shop if you don't know how.
Secondly, while it's okay to run recirculate occasionally, do switch to fresh air as much as possible. At the very least, do that some distance before you reach your destination and make sure you shut off your car with the HVAC on Fresh Air, not recirculate. This opens your HVAC plenum up to outside air, so any remaining moisture will have a chance to evaporate out. If I'm running A/C, which around here is probably 8-9 months our of a year, I usually shut it off before I reach my destination, so the ductworks temp has time to normalizes with the ambient temp, preventing condensation after I shut off the car, where the blower fan will not be running to blow it off.
If you already have a very strong smell, just spritzing cleaner or deodorizer into the vent can at best mask over the smell. Not much of it will reach all the way down the ductworks to reach to the plenum and evaporator coil.