I've never tried one with guppies, then again ... never tried guppies. My old HM never had a problem with it, nor did the CT before him. I've had one in my tank for a number of years and never had a problem with bacteria buildup and my HM loved to sleep on the gravel.
As before mentioned, I've never kept a guppy. I've always had a betta in the tank and by all accounts guppies and a betta are a baaad combination. That said, I don't know with guppies, but at least in my experience bettas do just fine with an under gravel filter.