PrBoom 2.4.1 (maybe older versions, too) does not depend on smpeg. - there is no occurrence of smpeg in the sources - I recompiled sdl-mixer without USE=-mp3 (thus getting rid of its dependency on smpeg), uninstalled smpeg and recompiled prboom; everything works as expected (sound, video, gameplay) BTW, there is a small typo in the ebuild. It says "# --disable-gl are threated the same", should probably mean "...treated...".
thanks, both fixed in 2.4.1 in cvs !