home-manager/docs/manual/faq/session-variables.md

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Why are the session variables not set?

Home Manager is only able to set session variables automatically if it manages your Bash, Z shell, or fish shell configuration. To enable such management you use programs.bash.enable, programs.zsh.enable, or programs.fish.enable.

If you don't want to let Home Manager manage your shell then you will have to manually source the ~/.nix-profile/etc/profile.d/hm-session-vars.sh file in an appropriate way. In Bash and Z shell this can be done by adding

. "$HOME/.nix-profile/etc/profile.d/hm-session-vars.sh"

to your .profile and .zshrc files, respectively. The hm-session-vars.sh file should work in most Bourne-like shells. For fish shell, it is possible to source it using the foreign-env plugin

fenv source "$HOME/.nix-profile/etc/profile.d/hm-session-vars.sh" > /dev/null