I have had them. They seem to cover the coral starting at the base and if you are not persistent at dusting the coral, it does start to shrivel and shrink.
They get so overpopulated that they seem to promote the growth of algae (not sure how, but they do).
I started controlling my population with a small air hose and sucking them out. They are attracted to light, so if you have one spot with a light on and the rest in the dark, the do tend to group towards the light. You will never completely get rid of them and you will have to perform a consistent maintenance ritual if you do this. Some fish/critters eat them, for example a six line wrasse does a great job (some will anyway).
Also, here is an alternative to flatworm exit. I have used it both wrong and right. The first time I used a heavy dose for 5 hours. This faded my sps cap's, but two weeks later they came back stronger than ever. As it was said earlier in this thread, they death of the flatworms has been the demise of systems. I say, clean manually first a couple times, then treat a light dose of Levamisole Hydrochloride multiple times.
http://www.reefcentral.com/forums/printthread.php?threadid=1379099&perpage=166
I see what you are saying about just letting them be. If you are filtering some of them out manually and they keep growing in your tank and reproducing, wouldn't that mean they are exporting nutrients from your system? Sounds logical to me.
Happy New Year!