On my NixOS, nix sets the environment variables XDG_DATA_DIRS, XDG_CONFIG_DIRS, etc. Maybe these contain what you‘re looking for? Do you have a path ~/.nix-profile/share/applications?
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I have this line export XDG_DATA_DIRS=$HOME/.nix-profile/share:$HOME/.share:"${XDG_DATA_DIRS:-/usr/local/share/:/usr/share/}" Do I need to add anything else? I do have the directory you have mentioned.
Which one in specific? There are some packages which maintainers did not bother creating xdg desktop specification... you can look into nixpkgs source code to see if they are specified there or not.
I do not know if Debian is able to pick the desktop files though
Adding those lines to .bashrc, helped with the flatpak commands. I can run them without having to type "flatpak run". I did this for nix: export XDG_DATA_DIRS=$HOME/.nix-profile/share:$HOME/.share:"${XDG_DATA_DIRS:-/usr/local/share/:/usr/share/}" However, I still cannot see the entries in rofi. The package is Chromium browser.