How to delete element in an array by id in nested object using custom data api

I am not asking you why you're doing this, but the technical answer to your question is:

db.collection.updateOne({"dataset_id": "4ac54805-18a2-46a6-afb7-8829eb0e1a27"},{"$pull":{"configurationDetails.fields":{"id": "0"}}})

It will remove the entire element of the 'fields' array with "id": "0"