I have UGF's on all my tanks. The normal down sides don't seem to be much of a problem, I have plants, IF they are getting into the plates it hasn't clogged anything, if I want to tear down the tank I am sure there will be roots broken, but that happens any way.
I use TimandKarens shop vac tip, and it works like a charm. My shop vac is 16 gallons, and I can use it two or three times in my 125 gallon tank, out with all the gunk, and it just takes a couple of minutes, not anywhere as long as using the syphon!
I've got MTS snails in all my tanks, and they work all through the substrate, and yes they get down under the filter, it's a bit scary thinking of them down there .......
The up side is that my tanks have more consistent biological filtration, with lots more surface to colonize bacteria.
