Nested JSON objects – do I have to use arrays for everything?

You don’t need to use arrays.

JSON values can be arrays, objects, or primitives (numbers or strings).

You can write JSON like this:

{ 
    "stuff": {
        "onetype": [
            {"id":1,"name":"John Doe"},
            {"id":2,"name":"Don Joeh"}
        ],
        "othertype": {"id":2,"company":"ACME"}
    }, 
    "otherstuff": {
        "thing": [[1,42],[2,2]]
     }
}

You can use it like this:

obj.stuff.onetype[0].id
obj.stuff.othertype.id
obj.otherstuff.thing[0][1]  //thing is a nested array or a 2-by-2 matrix.
                            //I'm not sure whether you intended to do that.