On my ~amd64 system no gui (mmg) is installed when I emerge mkvtoolnix-2.0.2 with USE="qt4 -wxwindows". It looks like nothing gets compiled in the work/mkvtoolnix-2.0.2/src/mmg/ directory.
mmg requires wxwindws... the qt4 use flag enables a GUI for mkvinfo... start it with `mkvinfo -g'.
comment #1 sums it up pretty well, mng is only available trough wxwindows, mkvinfo can use qt4 or wxwindows thus USE="qt4 -wxwindows" won't build mng but only a qt4 gui for mkvinfo
Please change the USE flag description to reflect that. I've just spent an hour trying to find out why no GUI was built for mkvmerge. The current USE descriptions are misleading because they're too generic.