I don't believe Backbone.js has any preference one way or the other. The way your JSON is structured is left entirely up to you. The first example works well if you're not expecting the comment data to outweigh the rest of the post's data. But if you're making something like Reddit where the number of comments is more than the number of characters in the entire post body, the relational structure is much friendlier to work with.
Backbone.js doesn't care how you structure your data because it leaves parsing and rendering the data entirely up to you. So pick the structure that fits your needs for the task at hand.
One thing I would change in the first example is removing the pointless "post" object wrapper:
{
"id": 404,
"title": "Hans shot first.",
"comments": [
{
"id": 4041,
"body": "But not anymore!"
},
{
"id": 4042,
"body": "Indeed he did."
}
]
}