Systemctl commands timeout when ran as root
Finally I've found the problem.
I figured that process 1 (systemd) was started with --switched-root and --deserialize. And as I found in that link it seems that there are some internal parameters which try to reload some previously saved state.
I've done a kill -9 on process 1 an now the systemd appears without the switched-root and systemctl is working again with or without rebooting.
Two alternative solutions to the problem:
1- rebooting with
systemctl --force --force reboot
2- without reboot, just moving session files
mv /run/systemd/system/session-*.scope /tmp/