The Japanese wouldn't take the risk, right now their missile shield is a two stage, they have the Aegis ships and the Pac-3. If they hit the missile in mid flight with a path over Japan there's a good chance that it will crash on the Japanese mainland and they have to hope that the Pac-3's that they deployed can intercept the debris. They don't have the Thaad system in place, but will probably get that now.
But I doubt that Japan bothers to shoot down a missile that's heading over their territory heading somewhere else.
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My name is Ozymandias, King of Kings;
Look on my Works, ye Mighty, and despair!
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