You need to switch from the built-in snes emulator to pisnes. It is an older emulator, so some newer games like SF2-Alpha and Mario RPG won’t work, but it is fantastic for fixing the sound.

Download the latest and install over top of what exists:

cd RetroPie/emulators/pisnes
wget http://pisnes.googlecode.com/git/pisnes.zip
unzip pisnes.zip
chmod 777 ./snes9x ./snes9x.cfg ./roms ./skins

Then you will need to edit ~/.emulationstation/es_system.cfg to use pisnes. Scroll down to the snes section and uncomment out the pisnes command.