Probably a dumb question but...
No such thing...only answers can be dumb, particularly when they are incorrect or mean spirited or made by politicians.
Running uninhabited water through a UV sterilizer has no effect other than wasting electricity and UV bulb life. There is no effect on the water, itself, other than the transfer of a tiny amount of heat. You could heat your tanks this way, but it would be about as effective as rubbing sticks together underwater. The point is there is no germicidal effect on water. When the water returns to the tank from the UV sterilizer it is just the same ole water that it was before its side trip.
Germicidal UV radiation does not affect water. It only affects critters that inhabit the water, if and when they pass through the UV sterilizer. Beneficial bacteria do not live in the water column. They live on surfaces of things such as rock, sand, glass, filtration media, etc.
Does this have an effect on beneficial bacteria??
Not really...Well, yes actually, if they happen to caught up in the water column for some reason, they could be swept up and radiated. But that is not where they spend time. If any beneficial bacteria do get radiated it would be a miniscule percentage of their population in your tank.
Furthermore, UV does not directly kill critters. It mucks with their DNA, gelding them, so to speak. The very few beneficial bacteria that may get radiated will be flushed from the UV sterilizer back into the tank to live out their happy little beneficial lives, but as eunuchs, and only if they are affected.
Not all critters are vulnerable to UV, particularly ones that are covered by or encased in protective gear...hard casings, shells. They sort of keep their DNA in the shade and get a free pass on the UV ride.
fab