Get the showsApplicationBadge value (that is what I requested this one and not setShowsApplicationBadge).
Reading through Apple reference material, it seems this preference could be retrieved by reading showsApplicationBadge (I have opened bug 1071494, as we are not able to read it from an XPCOM application, AFAIK). User can disable this sound as I said in previous comments.
The sound which is annoying user (confusing, in fact) is coming from OS X when we update the text on the badge.