How do I get Guix to have flatpak application show up in the applications menu whenever I install a flatpak application?

[trev]

You need to make sure your XDG_DATA_DIRS env var is set correctly to include $HOME/.local/share/flatpak/exports/share.

There should be a script .guix-home/profile/etc/profile.d/flatpak.sh that does this for you.