I finally found why the icons were not displayed. I had to set these variables for Gnome:

XDG_DATA_DIRS     For example,  /usr/share
XDG_CONFIG_DIRS should point to xdg directory.  For example, /etc/xdg

I also had to set XDG_DATA_HOME=/usr/share. shared-mime-info apparently cannot find its files unless this is set? Setting this also reenabled sound.

I don't know if these are necessary if Gnome is in /usr, but I have Gnome installed in a non-standard location at the moment.
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