no doubt you have probably done your research on what is required as in UV exposure and wattage for your targeted usage, in case you need a reference here is a chart i found while researching UV sterilizers which gives a guide to wattage, flow and exposure for target.
Reef Tanks: A UV Rated in the 30,000 to 45,000 columns is ideal for the reef environment.
UV’s rated at higher kill rates will destroy the planktonic food supply for the reef.
Marine Fish Tanks (No reef or Live Rock): A UV rated in the 75,000 to 90,000 columns will be the most effective at controlling fish disease.
All UV dosages are calculated at the end of lamp life (14 months).
Flow rates and results may vary.
This chart above is from the Aqua Ultraviolet website.
In my research i found many people using UV, some run permanently some run for a few hrs per day or a few days per week, it really depends on what your Display is stocked with and what it is you want to target, as mentioned beneficial bacteria tend to establish habitat on surfaces and not the water column so i would not be too concerned as far as terminating them. Some users of UV limit exposure or operational periods to preserve pod populations too, so there does not really seem to be a hard and fast rule as such but more finding a happy average for your particular needs and type of Display you are running or what the issue is you are targeting.
Anyway you are probably aware of all of the above, i see UV sterilizers as an important tool in Marine Husbandry, and flexible, if you fit gate valves on the output or input, or if you use a DC pump, simply tune it down with the controller to effect your chosen target function.
Hope this is of some small help.
Regards
B.