/etc/apache2/conf.d/userdata/ssl/2_4/*username*/whatever.conf
/etc/apache2/conf.d/userdata/std/2_4/*username*/whatever.conf
in the conf you can put :
<IfModule mod_userdir.c>
CustomLog /dev/null combined
</IfModule>
ssl folder is with ssl - std folder is without ssl. By putting the conf in the username folder it means it applies to all domains that username owns. This will stop domlogs for ssl, std, and your bytes log (you won't have bandwidth stats anymore in whm/cpanel). There are other ways to do it so only the ssl log, only the std log, only the bytes, log or any combination of those are changed. You can read more at
https://docs.cpanel.net/ea4/apache/modify-apache-virtual-hosts-with-include-files/
Remember to rebuild httpd and restart after making any changes.
To rebuild the httpd.conf file, run the following script:
/usr/local/cpanel/scripts/rebuildhttpdconf
To restart Apache, run the following script:
/usr/local/cpanel/scripts/restartsrv_httpd
With that said, I would still like to know why removing the CustomLog entries from the templates files does absolutely nothing. It is much easier to use that method then create all these folders and conf files in 'userdata' if you want to remove from all accounts.