We set up a different log file for each virtual host. Works just fine. Simply set
Code:
ErrorLog logs/domainname-error_log
CustomLog logs/domainname-access_log combined
(where domainname reflects the ServerName), in each VirtualHost container,
You could also do what you propose and have a sub-directory for each domain, but I think that would be unwieldy. Naming the log files per domain works well enough.
You could even point all domains to the same log files...but that would be VERY confusing should you need to troubleshoot a specific domain, so I say don't do that!