I did it and really wasn't sure it helped. I've heard from others who did also and said there was no obvious benefits to them. The one thing I was concerned about before I tore down my tank was that one is supposed to replace it after a period of time. With 2" of it in my fuge, with countless other critters, rock, rubble, macroalgae, end etc., I was not looking forward to emptying it and replacing it with new miracle mud. I'd go with a sand bed next time I set up a tank.
Also, I had my fuge, combo sump on a 155g drilled tank with a Mag 15 pump as a return and flowing thru my fuge. No problems at all with water going thru it too fast.
"Life may not be the party we hoped for but while we are here we might as well dance!"