UV can and are utilized on all types of setups....I used one on my 240 reef with no ill affects.....The problem is most people don't have a true understanding on how the units work, or how to properly use them......They have to have the correct flow through the unit, and that can vary from manufacturer to manufacturer, and depending what your trying to eliminate in your setup. You also find that most people plumbed them up and forget about them, till the bulb dies.....UV's do need to be serviced/maintained just like our other equipment we use. The bulbs or quartz sleeves which covers the bulb needs to be kept clean for the unit to be effective at it's job. Most don't do this. Why??? Because it's a hassle. On my unit I run I have a wiper which allows me to clean the sleeve without taking the unit apart or shutting it down. A lot of the units on the market down have the wiper which is a good feature IMHO......
With all that being said, there are reasons people choose to run UV's. Most think or are under the impression that it will eliminate or eradicate parasites or disease from the aquarium.....For this to happen the "bad" has to be in the water column and "free floating" and must pass in front of the bulb to be "killed" or "genetically altered". So we use ICK for instances....depending which stage the ICK is in, the UV is worthless. If your using it for water clarity your water flow needs to the unit changes as well, and does aid with water clarity, but there are other means to get water clarity if you choose to do so..
UV's don't and can't discriminate between good and bad that passes through the unit, so it will kill or alter all that passes in front of the bulb.