You're right that such tools will only work based on links between the pages. If a page has no other pages pointing to it, it's "invisible" for HTTrack (and other "spider" tools). If you know the URLs to this "unlinked" pages, you add them manually.
However, if the webserver has "Directory Browsing" enabled, by pointing to a URL containing a directory and no page name, it will display a list of all files in the directory. But it's seldom activated for security reasons. Most of the times, if no page name is specified, the webserver will serve a default page (index.html, index.php, default.html, ...) instead of the directory content.