GDM uses Wayland by default so random services that expect X server will not work. Furthermore, to support both X server and Wayland GNOME is not supposed to be controlled through X-specific settings but rather through gnome-setting-daemon, which abstracts many of the low-level details.
If you have home-manager enabled in your NixOS configuration, you should be able to just set the following for gdm user:
dconf.settings = {
"org/gnome/settings-daemon/peripherals/keyboard" = {
numlock-state = "on";
};
};
Edit: the settings were moved, see the comment below.
It is possible to achieve it without home-manager but it requires a bit more code, see the last paragraph in Need help for NixOS Gnome scaling settings - #5 by jtojnar.