For cyber-physical systems, cyber-security is vitally important. There are many cyber-security tools that make communications secure -- e.g., communications between sensors and the computers processing the sensor's data. Most of these tools, however, are based on RSA encryption, and it is known that with quantum computing, this encryption can be broken. It is therefore desirable to use an unbreakable alternative -- quantum cryptography -- for such communications. In this paper, we discuss possible consequences of this option. We also explain how quantum computers can help even more: namely, they can be used to optimize the system's design -- in particular, to maximize its security, and to make sure that we do not waste time on communicating and processing irrelevant information.