root cron shell_exec disabled warning

I have cron set in /var/spool/cron/root
I have cron file at /usr/local/cpanel/whostmgr/docroot/cgi/customcronfile.php

When cron runs it creates

PHP Warning: shell_exec() has been disabled for security reasons in /usr/local/cpanel/whostmgr/docroot/cgi/customcronfile.php on line 22

In customcronfile.php, starting at line 22 I have command
$ls = `ls -la /var/cpanel/users`;
$lslist = explode("\n",$ls);

 

Yes, cron is self running every morning and with every run it will write that error into log.
Im running somekind of custom command that will get status of inodes usage per user and outputs it into WHM.
shell_exec is disabled for php in php.ini, yes. I thought root can bypass this. I don't want to risk server security. Or wouldn't this be much of a leak?