Test launches of ballistic missiles these days are done with dummy warheads (for good reason); if the missile gets away from you and lands on foreign territory with a live warhead, it could start a war. Also, it it failed to detonate, your enemy could pick up your rocket and know exactly what you had for a warhead. None of the N. Korean missile tests launched over Japan have include a live warhead, AFAIK.
Maybe I missed, but I didn't see where the KT article says the warhead was either live or a dummy.
Is it possible it could have been a dummy, that was self-destructed by remote?