The argument here is approximately this: as solving jigsaw puzzles has been dramatically improved recently, you never know, maybe manufacture of weapons of mass destruction will suddenly get really easy overnight, resulting in an apocalypse.

What Joux and others have done is both important and impressive. But it simply isn't the same as breaking secure cryptosystems. The analogy between the two is simply overplayed.

Did people have reason to believe that the systems Joux and co. can crack were hard? No, despite not knowing how to crack them. Do people believe that their more secure cousins are hard? Yes, they do.