New Mikrotik version came out and my firewall was just a bit too tight
to allow remote WinBox connection. But I did have SSH...
And yes, upgrading to new version is easy enough from command line too. It's
just that one needs to execute two (you can omit the check) commands for the
same GUI experience.
/system/package/update check-for-updates /system/package/update download /system/reboot
And that's it, the new version is in.