Well I did some research and it looks to me that both mupen64plus & Citra standalone have problems with audio output. My workstation runs those fine unless I try to set the audio to hdmi output which is basically not detected at all. It just lists the onboard audio devices. It looks like at least citra had some quirks in the past with automatic audio detection SDL2: Selecting an audio device · Issue #1838 · citra-emu/citra · GitHub and so they ended up with an option to chose the audio device. But as stated before if your device is not listed you can't chose it as an output.
So all in all it looks to me it's something that GitHub - m64p/mupen64plus-gui: mupen64plus GUI written in Qt5 & GitHub - citra-emu/citra: A Nintendo 3DS Emulator have to fix in their code by proper detecting all output devices since Dolphin uses QT/SDL and just works
But maybe reworking the asoud.conf like this could also help but my knowledge of ALSA is somewhat limited https://wiki.archlinux.org/index.php/advanced_linux_sound_architecture/troubleshooting#hdmi_output_does_not_work
Maybe you could give this a try too:
https://download.nvidia.com/xfree86/gpu-hdmi-audio-document/#_alsa_default_device
But make sure you set RR_AUTOCONFIG_SOUND=false if you manually alter the asound.conf file!