Definitely if the files a confidential, place them outside the web root. This way you can control access trhough a single script. Knowing the password for .htaccess would still not allow them to get the files unless they were in a specific sequence.
To REALLY protect the files, you would chmod them to something only root could access. Then you could create a php file which ran server side, owned by root, and call it by system() command.
Sam