If you're asking if it's possible to break the encoding on an IonCube-encoded PHP file, then I'm sure the answer is yes. Any form of encryption can be broken, given enough time and resources.
You'll have to evaluate their encryption methods for yourself if you want to know how safe it is. If you can find examples of it being broken on Google, then maybe it's not the way to go. On the other hand, maybe those were just edge cases, or cases of someone getting their hands on the encryption key?
You'll have to weigh the perceived security of the product against your client's needs to use it. No solution is 100% once the code has left your hands.