Sometime in the cPanel, MySQL databases show 0MB of disk space used, when you know your databases are much larger. This is due to an option in cPanel that you specifically have to enable. To enable MySQL disk usage tracking:
Edit /var/cpanel/cpanel.config
Change:
disk_usage_include_sqldbs=0
to
disk_usage_include_sqldbs=1
Then run the following:
/scripts/update_db_cache
Thats it..