dbus[X] was added to RDEPEND because virt-manager incorrectly used dbus-launch instead of dbus-run-session when saving configuration on X11. This is not the case anymore and saving configuration works for x11-forwarded sessions without dbus[X].
also slightly related:
Steps to Reproduce:
1. Install virt-manager
2. emerge -C virt-manager and rebuild dbus without USE=X. Don't run --depclean
3. Download virt-manager 4.1.0 release from github and start it over ssh with X11 forwarding