Finally I found the issue. The location for .ini files for ZTS modules is different. I have installed both modules in the right places and ioncube loader is working perfectly now. For compatibility reasons I prefer to stay with apache (worker MPM) + libphp5-zts. Still testing.
Why shouldn't I use Apache2 with a threaded MPM in a production environment? PHP is glue. It is the glue used to build cool web applications by sticking dozens of 3rd-party libraries together and making it all appear as one coherent entity through an intuitive and easy to learn language interface. The flexibility and power of PHP relies on the stability and robustness of the underlying platform. It needs a working OS, a working web server and working 3rd-party libraries to glue together. When any of these stop working PHP needs ways to identify the problems and fix them quickly. When you make the underlying framework more complex by not having completely separate execution threads, completely separate memory segments and a strong sandbox for each request to play in, further weaknesses are introduced into PHP's system.
If you want to use a threaded MPM, look at a FastCGI configuration where PHP is running in its own memory space.
Yes I understand, but nothing has changed in this regard. "Apache 2" refers to the 2.x line of Apache. I use Apache 2.4 also and it's amazing with php-fpm...a similar performance to nginx with php-fpm.