This is what Godaddy support answered:

The ionCube Loader is already supported by default with our Linux hosting packages. However, the settings for the ionCube Loader are disabled if you are using PHP 5.

We have recently upgraded PHP to version 5.2.5. You will want to make sure you are using the appropriate binaries for PHP 5.2.5 and update any php.ini references to the old version of ionCube. You can review the ionCube binaries at:

• http://www.ioncube.com/loaders.php

Does that mean that I don't have to call the loader in my PHP.ini???

Thanks!