i am confused on what you mean by beneficial bacteria, and how are they not as susceptible to UV as harmful bacteria? do beneficial bacteria have shields on them to reflect UV that the harmful ones do not? if the UV is strong enough to kill bacteria, it is going to kill all of the bacteria. it does not matter if we think they are beneficial or harmful.
how is running lets say 200gph through a 100w UV going to do anything to the critters in the system that are not able to fit through the UV? it may kill off anything that goes through the UV, but if these affected organisms and organics are removed quickly from the system (why i would recommend running the exit water from the UV directly into a skimmer), then how is this going to do any harm to the system, if not help the system by making the skimmer more effective at removing different types of organics.
G~