Hide My WP adds a redirecting layer over WordPress to let you customize the old paths without physically change them.
It also gives you the possibility to disable access to the old paths for hackers and protect the WordPress plugins and themes.

 

WordPress Directory Structure

 

All these changes will not affect the WordPress directory structure through FTP and it will not break it in case you deactivate the plugin.

It looks like a simple plugin but it’s a complex system behind it and a good firewall against Script Injection and Brute Force attacks.