I got some coffee in me and narrowed down the problem: the postinst file in libvirt-daemon-system was changed from just starting libvirt-guests.service to restarting libvirt-guests.service. libvirt-guests.service now shuts down all VMs but the autostart mechanism of libvirtd doesn't kick in because it was only a service restart, not a system restart.
I got some coffee in me and narrowed down the problem: the postinst file in libvirt- daemon- system was changed from just starting libvirt- guests. service to restarting libvirt- guests. service. libvirt- guests. service now shuts down all VMs but the autostart mechanism of libvirtd doesn't kick in because it was only a service restart, not a system restart.