Ok - it wasn't Suhosin's fault.
After a while the problem showed up again. The CPU skyrocketed every time a PHP script was called.
What we did: We disabled all unneeded Apache modules and the same with the PHP extensions. We also removed Memcached.
For now everything is fine and the CPU is at 0 - 1,2 % which is perfect. We still have no idea what was wrong.
Once we have a clue, I'll post an update.
Hope this is helpful.