(Sorry for double posting can't edit previous post).

WHM logs, along with Apace logs are in /usr - cPanel logs /usr/local/cpanel/logs/ , Apache /usr/local/apache/logs/ - his /usr is mounted on a separate partition from /.
So no need for log rotate. Most problems cause Apache DOM logs that can grow to several GBs if DOM log clearing isn't enabled in WHM when stats are run.