I’m trying to upgrade from using the V1 to V2 Square APIs, but I’m not seeing any documentation on a V2 API for webhooks. Does anyone know if something like this exists?
Currently there isn’t an API to subscribe to v2 webhooks. To subscribe to events you will need to do so in the Developer Dashboard. 
What if I need to do that programmatically?
For example, webhooks for our app will need to send to a unique URL per installation. That doesn’t seem possible to do in the developer dashboard.
Also, is the v1 webhook API deprecated?
At this time programmatically setting a unique URL per installation for webhooks isn’t currently available.
Yes, all v1 webhooks are deprecated.
I am shocked and dismayed to find that out.
For each installation are you using OAuth?