I have ISPConfig 2.2.6 with Webalizer installed. stats folders are created in all sites' roots, but they are empty, with the exception of .htaccess files. What I see though is a directory /var/www/usage that has up to date stats, but, obviously, I cannot access it via browser. And it looks to be server-wide and not specific to any site in particular. Can I create a webalizer.conf for each site?
ISPConfig is handling all this automatically and the /var/www/usage directory is not from ispconfig. Take a look of your syslog to find out why the log splitting cronjob is not executed on your installation.
Installed ISPConfig 2.2.29 last night, and this morning the stats are being generated for all sites. I guess some config was not right during the original install.