You mean flags like nwg-hello -c <config-file-path> -s <style-sheet-path>, right?

Yeah and the same thing but for setting the path to where your style is located like nwg-hello -style or whatever to set the styling path

I have no idea what your problem with editing files on nixos is, but this will require edition of the /etc/nwg-hello/hyprland.conf file, for it to look something like this:

monitor=,preferred,auto,1
bind = ALT, Q, killactive,
misc {
    disable_hyprland_logo = true
}
animations {
    enabled = false
}
exec- -c /your/path/here -s /another/path/here; hyprctl dispatch exit

Is it going to be possible?

Sadly that's not possible. We cannot edit our files, we can make new files though. That is because nwg-hello is within the nix/store directory which is read only, so there is no singular way to change it. Except possible commands

Maybe an environment variable would be a solution? Are you allowed to set e.g.:

NWG_SESSION_DIRS=/usr/share/wayland-sessions:/usr/share/xsessions (use your actual paths here)?

If I'm correct we are allowed to set variables with the export command. But how could we fix the css as well?

By adding another env variable. But the most obvious solution would be just patching the config file by the packager, for it to point to proper locations.