Okay fellas, I emailed this concern to my bio professor I'm doing undergrad research with.
this is his reply :
 Hey,
  Great question.  I have mud on the bottom of most of the tanks in 101,
and in fact, it does trap anaerobic deposits.  Sand does a fair job of it
too, especially the fine stuff.  Whenever I clean out, or stir, one of
these aquariums, I get a little whiff of hydrogen sulfide.  so, yeah.
thing is, I have never ever known fish to be harmed by it.  Can you
imagine?  In the wild, if a little bubble of swamp gas killed fish?
I don't know what you are keeping, but the usual aquarium species can take a
little harmful gas.