Well, nothing is full-proof. There are measures you can take:
1.) Always disable directory listing and hotlinking to your "include" directories
2.) Never save includes with the extension "inc", save the as "inc.php"
3.) Use permissions for your include directory
4.) Use common sense
If you just think about it, the hackers that want to get in will not necessarily get your included files (since they can't tell that an outside inc file is included via PHP). Most hackers attack via SQL injection.
~Brett