Follow the below steps and reslove the issue :-
In cPanel >> mysql databases, it’s display database size as “zero” even if it is not.
You just need to make the below changes to fix it :
# cat /var/cpanel/cpanel.config | grep disk_usage_include_sqldbs
disk_usage_include_sqldbs=0
Now we can see disk_usage_include_sqldbs=0 ( set it to 1 instead of 0 )
After that just run the below command
#/scripts/update_db_cache