Before side-channel attacks, the open crypto community did not think about using information other than the plaintext and the ciphertext to attack algorithms. After the first paper, researchers began to look at invasive side channels, attacks based on introducing transient and permanent faults, and other side channels. Suddenly there was a whole new way to do cryptanalysis. Several years ago I was talking with an NSA employee about a particular exploit. He looked at me as if I'd just arrived from Neptune.
Conventional engineering is about making things work.
It's making sure security isn't broken, even in the presence of a malicious adversary who does everything in his power to make sure that things don't work in the worst possible way at the worst possible times. A good attack is one that the engineers never even thought about. Defending against these unknown attacks is impossible, but the risk can be mitigated with good system design. It's designing the entire system so that when the unexpected attack comes from nowhere, the system can be upgraded and resecured. This isn't a temporary problem.