No! This is as much a conceptual mistake as "interceptor costs 10X as much as the missile it is designed to destroy, so antimissile defense is foolhardy" without taking into account the value of what the missile can destroy.

Maybe the boat will get through; maybe it won't. The ship might be intercepted before it reaches the target. Or security personnel with geiger counters can find it on the dock. And so on. From North Korea's perspective (or the USSR's during the Cold War, or Russia or China now), the uncertainty of the success of such an attack makes it very, very risky to actually deploy, except maybe in a situation where you're already losing the war (and in that scenario, the odds of a successful detection by the target are obviously that much higher).

A ballistic missile, by contrast, cannot be stopped except with great, great difficulty. That's why North Korea has built missiles for its nukes, and not a fleet of cargo ships and fishing boats.