So, you want to save things in Godot.
This is my general advice over this topic is this post.
Objects' properties contains a lot of information that you may find useful when you're writing things to save other project things.
Something good about using resources (and File/ConfigFile) is that the thing that writes it to disk is aware about that information, and try to save it with the included data, something that you has to do manually with custom formats (like JSON).
Generally speaking, I don't use JSON when is not necessary (like, when I don't need to transfer data between two apps), I prefer YAML or INI style format (and is a personal thing, is ok if you use whatever you want to use).
Edit: Forgot to upload the pic that is on the post 