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Those "two" versions you're seeing are two ways of describing the same files. In Redhat Linux for example (which you might be using) the directory "/etc/httpd/logs" is a symbolic link to /var/log/httpd - i.e. an alternate name for that directory.
So there's only one copy really, and it only uses one lot of space. If you have shell access to the server, you can see this with the command "ls -l /etc/h*".