How many people actually used Python's MSI library?

It was Windows-only (presumably a wrapper around the native tooling), and was primarily for creating Python's own installer, which apparently doesn't get built as an MSI anymore.

I use it for packaging my Python application. But it seems pretty low-level, so I suppose I could call the win32 API directly through ctypes when they remove it.

You've been able to do Win32 stuff in an AppX since early in Windows 10 history, it's mostly "unsandboxed". MSIX, the "new" AppX, has Windows 7/8 support for Win32-focused installs in preview.

Semi-relatedly, Microsoft has already been exploring with the Python team MSIX deployments for the Python interpreter itself (you can even find it in the Microsoft Store now on Windows 10, and typing `python` on a command line in recent builds of Windows 10 will auto jump you to the Store if you don't have a python.exe in your PATH/installed).

(Also, getting in the weeds, the "mostly unsandboxed" refers to that MSIX installs will do a few things to insure at all costs clean uninstall, including system folder virtualization/redirection, registry virtualization/redirection, and similar techniques. Windows and MSI has been doing a lot of this sort of thing under-the-hood silently since XP as a part of compatibility work, MSIX just does it more obviously/automatically/always.)