ionCube and Codeigniter

I would exhaust all other methods of increasing security before considering encrypting the source code using something like ionCube.

PHP code should never be displayed when deployed to the end user if PHP is installed correctly and the file extension is .php.

Hiding source code in case someone gains access to your server might add a small layer of security for the code used; however as most data is typically stored in a database (which is easy to access once the server is compromised), there is very little reason to encrypt the source code itself unless the code itself is vital to an organisation.

From a security standpoint it may add a layer of protection, but it also adds extra development time ( any updates have to be made on the original source code and then encrypted before being pushed live ) and a small hit to performance.