>>"Would you not be just running / washing cleaned water over them?
Hopeing that you wash off any bad bugs?"
Yes. In part, the same, using sterile saline, is often done to clean wounds. It's called irrigation. It works. It works better if it's done with a larger volume, a more forceful stream, and a longer period of time. The surface of plastic threads though don't bear a close resemblence to the tissue of a wound however. I'd expect irrigation to work a little better on the threads, but it would be nice to have empirical data to go by.
This subject came up last week (or the week before, i forget precisely when) in another Thread. You could do two things to minimize your concern.
First, screw the cap on and off several times BEFORE dosing your water vessal with UV-C. The hope here is that the "pumping" action caused by the repeated screwing on and off of the cap will pump/force any water out of the threads - either into the undosed volume of water, or out of the container threads and cap threads into the "outside" world. Then dose with UV-C. The final replacement of the water container's cap would hopefully have little water left in it that would possibly be pumped into the water container when the cap is screwed back on the container.
Second, you could do what I do. I have "sippy" caps with poly tubing "straws" sticking out of the cap. My lips/mouth never contact the possibly untreated, contaminated threads.
Just some thoughts.