As of 1.27.0-wmf.22 (deployed to WMF wikis April 26-28) and MediaWiki release 1.27 (specifically, this change in Echo), meta=notifications will return its result as an array rather than an object.

Previously, the meta=notifications output looked like:
{
    "query": {
        "notifications": {
            "list": {
                "12345": {
                    "id": "12345",
                    "type": "edit-user-talk",
                    ...
                },
                ...
            }


Now, it looks like:
{
    "query": {
        "notifications": {
            "list": [
                {
                    "id": "12345",
                    "type": "edit-user-talk",
                    ...
                },
                ...
            ]

My apologies for the late announcement, and thanks to APerson and Cienca Al Poder for noticing and encouraging me to write this announcement.