Ioncube is part of CBSubs security to minimize potential damage to your payments in case of site hacking. Thus it is a prerequisite.
We have seen many hosts which run both Zend and Ioncube on the same host, provided that the PHP installation, and Zend optimizer are up-to-date and compatible, which often isn't the case, as Zend had over a year delay in supporting latest PHP versions.
Additionnally to the hoster system-based installation, there is a folder-based installation that is possible as well, and that is described in the readme file of the free ioncube loader package available here (you need to know which system the hoster has on your server, usually Linux (x86), sometimes 64-bit version of Linux: Linux (x86-64)):
www.ioncube.com/loaders.php
It is enough in most cases to do that folder-based installation that you can do yourself.
If you still have issues, please private-message to Kyle (krileon) of our team the access and URL to this thread for reference, and we will help you.