When you don't need a standard format, Godot's INI implementation (ConfigFile) is a superior format to JSON :)
While not standardized, ConfigFile can be used to serialize any Godot datatype without having to convert it to a string or an array/object first. Also, unlike JSON, it features an actual integer type, which prevents bad surprises when saving and loading configuration.
Even if you intend to write ConfigFiles by hand, it's more permissive than JSON. For instance, it allows adding comments to your files (which will be lost when saving, though).
Still, Godot supports JSON using the JSON class.