I've read a number of posts on other forums that a UV sterilizer is very important for bare bottom tanks. The idea is that the UV helps break or weaken some of the molecular bonds within dissolved organic compounds. In short, the UV can help to improve the efficiency of your protein skimmer.
Yes, the flow rate through the UV does need to be on the slow side, and is best plumbed on or off the drain line.
IMO, they do not harm anything in terms of a reef environment, and can only really help. The amount of heat they are going to add is negligible. I say, if you've got the money for one, then add it.
As for the idea that a UV is going to destroy good bacteria too, well yes thats true, but the large majority of your beneficial bacteria's are found within your LR (and LS if you've got it). A UV isn't going to change that . . . .