You can increase the log processing frequency for web statistics via "WHM Home » Server Configuration » Statistics Software Configuration". This will retain the Apache domain access logs for longer periods, but also result in delayed statistic processing for your users. Additional options available under the "Stats and Logs" tab in "WHM >> Tweak Settings" include:
Delete each domain’s access logs after statistics are gathered
Archive logs in the user's home directory at the end of each stats run unless configured by the user.