How can nested subdirectories and symbolic links be used without conflict with a multi-site Drupal installation?
Are you using just one rewrite? I have this exact setup, and I take care of it with a separate rewrite for each sub-directory. If you just use the default index.php rewrite, the path gets rewritten back to the default, like drupal.drupalsite.com/index.php?q=/campus/news which is where the 404 comes from. I also use aliases in the server level config instead of symbolic links. It makes things cleaner. (Alias /campus/bus /var/www/html/whatever)

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} /campus/bus/
RewriteRule ^(.)$ /campus/bus/?q=$1  [L,QSA]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} /campus/news/
RewriteRule ^(.)$ /campus/news/?q=$1  [L,QSA]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} /
RewriteRule ^(.*)$ ?q=$1  [L,QSA]