After contacting IBM support, I learn the following:
The registry backup command would only run on a box that has been declared (in the ClearCase Properties in the Control Panel menu) as a registry backup server. Consequently, it cannot be the existing registry server. So running the registry backup command from the server itself (as it's configure now in the ClearCase scheduler, as a Daily job) will have no effect, and produces no log.
The registry back-up is only copying the files located in
$CLEARCASE_HOME\ClearCase\var\rgy from the ClearCase registry server to the
$CLEARCASE_HOME\ClearCase\var\rgy\backup folder on the backup server.
If there is no registry backup server, but the files are backed-up another way (i.e on tape), then copying them on any ClearCase box in the
$CLEARCASE_HOME\ClearCase\var\rgy\backup folder and then using the
rgy_switchover command will do the trick.
In all cases, all the Client would have to be reconfigured to point to the new registry server, so it's not really a hotswap.
Finally, if the registry server is also the VOB server (like it is at most polaces), all the VOBs would have to be restored from the tape anyway.
All in all, it's no big deal to not run this command if the files are backed-up another way, and even if you run it, the registry switchover is still NOT a hotswap.
So to answer my own question: No I should not be worried ^_^ , the whole thing seems quite useless to me if you already are a good sysadmin doing backup of your servers.
References to registry backups can be found online on the IBM website