Earlier quoted context omitted.
I may be missing something, but how is searching an array of JSON objects more efficient than direct lookup by ID?
I agree with you. "OP" was referring to your suggestion. I edited my pervious comment to clarify.
It's important to note that the goal of JSON API is to be consumed by a general-purpose client (like Ember Data), so the JSON will likely be processed once and indexed as needed. In the system we extracted this from, the Array is loaded into a Store, which indexes the documents by type and id, so future lookups are quite efficient.