I just like the look of substrate in the display. As such I would probably always have it. I also think that a sand bed tends to increase the amount of pods and other critters, though I suppose thats debatable.

But BB offers some nice advantages, it does let you do anything you want with flow. You needn't worry about old sand being a nitrate time bomb, which they may or may not be, depends who you ask. I will say that if I had bb in the tank I would go with none in the sump/refurgium. There again I see no need for sand or mud, etc in the sump. You need a pretty big and deep sand bed to actually have any appreciable de-nitrification. A couple cc's of vodka per day can take care of nitrates.