Remember that it will only kill what passes through it, and not 100% is killed. Depending on the water flow rate, and the amount of time the bacteria is exposed to the uv light, not all organisms will necessarily be killed, you would have to adjust your flow according to the UV sterilizer Manufacturers Specs...
yes it will kill some beneficial bacteria, but since most of it lives within the filter, it won't be exposed to the uv.
I have one on my 125 gal discus tank, but dont run it 100% of the time.