Update:
It's a macOS Monterey issue, not an Apple silicon / Intel issue.
Also, I found out it has to do with having set NSApp activationPolicy to .accessory or .prohibited - if those are set, the app is terminated prematurely on shutdown / restart (-applicationWillTerminate: is never called).
If it's .regular, it works like it should.
Topic:
UI Frameworks
SubTopic:
AppKit
Tags: