MongoDB / Mongoose Schema for Threaded Messages (Efficiently)
On this particular topic you are in luck, there is a great post discussing the various approaches to the schema here (it's a slight twist on what you are looking at, but not much different):
http://blog.mongodb.org/post/65612078649/schema-design-for-social-inboxes-in-mongodb
Then, this topic was also covered in detail at MongoDB World 2014 in three parts by Darren Wood and Asya Kamsky:
Part 1 Outline and Video
Part 2 Outline and Video
Part 3 Outline and Video
Also at MongoDB World the guys at Dropbox talked about the lessons they learned when building their Mailbox:
http://www.mongodb.com/presentations/mongodb-mailbox
And then, to round it off, there is a full reference architecture with code called Socialite on Github written by the aforementioned Darren Wood: