Exactly. If the game supports in-game chat ala Destiny, Overwatch, CoD, etc. Inserting headphones into the switch will allow standard comms. Party chat will be done via the app.
I assume the game audio will sync to the app, allowing both chat and game audio to pass through, hopefully with a mixer to allow custom prioritization of chat/game-audio levels.
Do any of the tear downs look at how many connections the jack input has? The icon next the minijack input doesn't have a microphone, which my laptop has but neither has Wii U gamepad apparently.
It makes sense to not have one on the joycons. Since you hold them in multiple different ways, there's really no spot you can 100% guarantee will be unobstructed at all time.