MySQL uses no space on cPanel
For some reason cPanel decided to start by default excluding sql databases from the disk usage stats.
To enable these again edit the /var/cpanel/cpanel.config file and change disk_usage_include_sqldbs from 0 to 1.
After running /scripts/update_db_cache you should now see disk stats in the interface once again.
Note: SQL database usage stats can be quite intensive to calculate so you may want to leave it off.