And here is what seems to be a short explanation of the reason why Works with Nest is being shut down, and Google’s suggested method of how to control Nest devices: Routines
How is Works with Google Assistant different from Works with Nest?
Works with Nest allows many third-party partners direct access and control of your Nest devices (with your permission). Works with Google Assistant enables all your connected devices to be controlled by the Google Assistant through voice, the Google Home or Assistant apps, or through Home View on smart displays (again, with your permission).
From the Home or Assistant apps, you can set up multi-device automated actions, such as morning or bedtime routines, through Assistant Routines. Third parties will no longer be able to ask for permission to directly access or control your Nest devices, thus keeping your data more private.