You need the relevant enable options set to true, otherwise the configuration files are not created and symlinked to the correct location. You have the enable option for Hyprland commented out, and do not have one for Waybar.
Yeah, I kinda thought that just installed it. Since the system config had them installed I thought I shouldn't do it. Obviously I was wrong. I've fixed it now.
Yeah it's an easy mistake. For every program/service I know of in NixOS, none of the modules options will be applied if you don't enable it. Enabling it does also install it, so it's safe to remove from the system config if you want.