Yes, there is backward compatibility. That is, if you just update a Host and don't erase/touch its settings - it will retain the old ID. The old ID will still work indefinitely so you don' t have to change it. But if you change it, the new ID will be 12-digit and you'll also have to update the corresponding record in your Viewer address book (otherwise you will be connecting by the old ID code).
To sum it up, you can simply update your remote Hosts when you have time to do so - either manually or remotely through the Viewer and don't bother with the IDs at all. Performance-wise there is no difference if a given Host has an old or new-format ID code so long as the Host itself is updated to the latest version.