Basically, a UV is going to "nuke" anything that is free floating and goes through it. I have no idea about flukes, but its supposed to zap algae and Ick in the tomite stage.
It will definitely kill some of the good things you want floating around in a reef tank, so there's a fair amount of debate about the pros and cons there. In a FO tank, there's less impact, so some folks will say they are OK for FO, but not for Reef, others will say neither or both...you'll have to make up your own mind on that one.
If you search the Equipment & DIY section for " µw/cm2 " I posted a ton of information on all the research I did on them a while back.
In my setup, I have seperate returns from my sump and refugium- the refugium return bypasses the UV, so the little critters don't get zapped on their way to the main tank. Of course, if they go into the main tank, then get sucked down the overflow, they'll most likely end up gettied zapped, but then after a few trips through the impellers on the pump that may be moot.