This issue where database size show '0' in cPanel but tables, data exists in server. Here is the fix for it . Just follow the below steps,
1. Open cpanel.config file
#vi /var/cpanel/cpanel.config
2. Edit line and save the file (:wq) and exit.
disk_usage_include_sqldbs=1 ( you need to set it to '1' if '0' )
3. Once the editing has finished, please run following script,
#/scripts/update_db_cache
That it !