After upgrade to 2.4 $CLUSTER and $SERVER databases became visible in database list. While reboot temporarily hides $SERVER (it reappears after larger intervals of time), the $CLUSTER is visible at all times. Deleting the database doesn't solve anything as it just reappears in a minute or so. While not a huge problem it does confuse some administration software when they try to run certain commands on these servers and get errors.
No sharding or replication is active. The server is fully standalone. No database files for these dbs exists.