Per my comment over on #3066146, the subdir.d folder (using either Apache or Nginx) doesn't get cleaned up when a subdir site is removed. The subdir.conf file for the deleted site should be removed.
@ergonlogic suggests:
* that'd be a post_delete drush/provision hook, something like drush_subdirs_post_provision_delete()
* maybe take a look at drush_http_provision_delete()
* the base class that's responsible for the subdir vhost provides an unlink() method
Which sounds like a good way to go to me :)
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Comment #2
colan