That is very strange. Whatever happened to all warfare is based on deception. If I was in charge and we had decided to not intercept a missile firing, the last thing I would do is announce that fact. Shear stupidity. After the Norkies heard that statement, I bet one of their generals suggested capitalizing on this opportunity (more precisely described as a vulnerability).
Say if we DID shoot down the stupid thing at its last stage, who other than ourselves and Japan would know?
Depending on the parameters of the flight the missile was likely non-interceptable even if we or the Japanese had wanted to.
As people (should) know, we don’t currently have any operating weapons against boost-phase missiles. Any Aegis ships around Japan or Japanese land-based Patriots would only be useful against debris or stages landing near Japan.
The GBIs in Alaska would only be effective if the missile was actually approaching Alaska.
If the final stage was a re-entry vehicle in the middle of nowhere in the Pacific, we wouldn’t have had anything near enough for a mid-course intercept, and if it was a satellite launch, we couldn’t have intercepted it (the Lake Erie satellite shoot-down was a one-time hardware and software modification).