The ionCube Loader is a PHP extension which used to handles the reading and execution of encoded files at runtime.
Cpanel does support in build script to install it very easily.
1. IonCube when installed via EasyApache or the PHP Extension Manager (/scripts/phpextensionmgr) installs IonCube for use by PHP Applications served by Apache.
You can easily install it via ssh using following scripts
/scripts/phpextensionmgr install IonCubeLoader
2. IonCube when installed via the Tweak Settings option configures the Internal PHP environment to use IonCube.
WHM > Tweak Settings > PHP > Loader
Option 1 means IonCube is available for PHP Applications accessed like:
Option 2 means IonCube is available for PHP Applications access like
Option 1 is served by Apache, Option 2 is served by cPanel.