Hi,
When we come across to an issue like mysql dbs showing 0mb size, we can fix this issue by
1). Check the cpanel config file /var/cpanel/cpanel.config
2). Find and change the following directive value from 0 to 1 and save the file
disk_usage_include_sqldbs=1
3). Restart the cpanel by
service cpanel restart
4). Run the following CP script to update the stats
/scripts/update_db_cache
Now the databases are included in the used disk size calculations and the correct numbers will be shown in cpanel. By default this directive is disabled to decrease server load, as such calculations may consume great amount of CPU.