In order to find out where exo
reads desktop applications from, I had to run the application from my terminal using the command:
strace exo-preferred-applications 2>&1 | grep 'openat.*\.desktop'
This allowed me to identify two folders where exo
reads preferred applications from:
/usr/share/xfce4/helpers/
~/.local/share/xfce4/helpers/
Knowing this, I was able to either uninstall or remove useless desktop files which were cluttering the exo menu.