When to create a new INSTANCE ID?

Do we need to define in the configuration app an entry and an INSTANCE ID for each type of download/protocol?

or we can manage everything with simple WMS? when is it necessary to use other protocols?

You can have one instance for all types of protocols. Instance is actually just a link to the configuration, where you have your layers define.
Then you can use this for WMS, WCS, Python (it uses WCS) or similar. These separate only in the base URL, e.g.:

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