They're supposed to be! Each subdomain is treated as a separate domain with the www being default. Each can be hosted on a different server and each can have its own DocumentRoot, i.e., it's all required.
As for the <Directory> entries, they appear to repeat server configurations so, if you modify the server, they will be inherited (and your vhosts entries can change the default from the server). If they're set as you have them in the server, you can delete these as redundant.