Update: Apple Watch code has now been discovered in the latest update to Pokémon Go. From The Sylph Road
Many new references to the watch 'faces' and interactions are showing. Code to sync KMs walked has appeared, along with a few other tie-ins to the main app (e.g. the Pokedex). We are not able to see how Apple HealthKit has been integrated, and whether the watch itself will be involved in tracking KMs.
The main app will 'know' when a watch is paired with the app, and appears to be able to push notifications to the watch.
There have been some rumors circulating about Pokémon Go for Apple Watch being canceled or postponed. Don't worry! Far as I know, that's not the case at all. The app, which was shown off at the Apple Watch 2 event back in September, is still in active development.
So where is it? There's a certain amount of complexity involved in making Pokémon Go for Apple Watch. It ties into both the Apple Watch Workout system, which means you'll get credit towards your activity goals while out catching Pokémon, and HealthKit, which syncs all the information. The latter especially has some of the most involved privacy systems Apple has ever deployed, and my guess is Niantic and Apple are taking the time to make sure all that integration is done right.
Regardless, Pokémon Go for Apple Watch is still on track for a 2016 launch. And that means we should be hunting happily from our wrists before the fireworks go off for New Year.
Update: Pokémon Go has confirmed the Apple Watch app is indeed coming soon.