Hide unwanted .desktop files.
The application-cleaner is a script which runs using a pacman hook whenever a new application is installed adding a .desktop file. It will loop over a list of provided configuration files and append the content of each config to the matching .desktop file.
You can find a pkgbuild file here.
Add config files with the below content to /etc/arkane/application-cleaner/. The filename should match the name of the .destkop file in /usr/share/applications.
contain='NotShowIn=GNOME;KDE;Pantheon;'