To be totally honest, I don't know if they are making a difference or not. My nitrate and phosphate levels have always been undectable and I always ran carbon and GFO...and I still do even with the bio-pellets. There may be an improvement in the SPS colors, but it's nothing drastic at this point.
I've read where people had cyano problems or their water getting cloudy when they started running them. Neither has happened to me. I do have the output of the bio-pellet reactor at the input of my skimmer pump and the skimmer doesn't produce quite as much skimmate as before, but what it does produce stinks so bad it wants to make you puke (not that it smelled like roses before).