That might work as a first strike capability - although sailing a cargo ship from North Korea to Tokyo without garnering any interest from intelligence agencies might be more difficult than you give it credit for.

But the main thing you want nuke for is as a deterrent. Get in a fight with us and we press the button. It's hard to imagine the sneaky boat trick working when North Korea is under blockade by the entire US and Japanese navies. And even if they run the blockade they're going to have trouble getting close to Tokyo.