All the good bacteria is attached or embedded within your live rock, substrate, media, bio pellets, etc. Very little good bacteria, if any, are free floating in the water column. It’s the bad bacteria or protozoans (like ich in the free swimming stage) that are in the water column that UV reduces.
The only negatives to running UV I’ve experienced are to your wallet ... and an extra piece of equipment to service. They have to add some heat to the system, but not to the extent I’ve been able to measure or notice.
