I remember that the subwiki concept first appeared in TidGi-Desktop. It was designed to add a private folder for users. Even if the HTML is exported, the content in the private folder will not appear in it. The folder structure is roughly like this.
/subwiki
/tiddlywiki.info
/tiddlers/subwiki(soft link)
The usage is to add a private tag to a tiddler(in tiddlywiki-app)