I have an engineering background, but very very new to iOS development.
Welcome! Unfortunately it’s not good news on this issue...
our organization built has a dependency to UIremotekeyboardwindow, which i'm told, will no longer be supported after iOS 16 is released.
Actually that was never a supported API and should never have been used by apps in the first place. It’s an internal implementation detail of the OS that people have figured out how to exploit over the years for various purposes. But since it’s not a public API, it could get changed any time and break apps that use it. Apps should use only public, documented APIs.
What exactly did the existing code accomplish via this API? There may, or may not, be a way to do it via public APIs.
should we expect all apps that use this class to crash once a phone is updated to iOS 16?
It depends on each app. If designed to fail gracefully (and simply lose the relevant functionality) then great. Or if never designed to handle the case of it no longer working on future OS versions, then not so great.
See this thread for a longer discussion of a similar issue. The solution may even be relevant to your situation.