Sometimes you may see the mysql database size as zero in cPanel

This can be fixed as follows:

SSH to your server as root and edit the cpanel.config file

vi /var/cpanel/cpanel.config

and search for

disk_usage_include_sqldbs=0

and change to

disk_usage_include_sqldbs=1

If the parameter is not present, add it. Save the file and execute the following command:

/scripts/update_db_cache

This may take few minutes to get fixed if you have a large number of users with databases, but once done, we should be able see the database disk usage show up accurately in cPanel.