That's not how things work, at all. Ballistic missile defense is meant to reduce the number of nuclear warheads that make it through, not eliminate the threat entirely. Extant ballistic missile defense doesn't even come close to eliminating the threat, and that's without considering Status-6.

Consider, for instance, that there is no way in hell you could touch North Dakota with Status-6. If Russia wanted to attack missile silos in North Dakota, they would need to use their own ballistic missiles for it. Ballistic missile defense reduces the chance that they could succeed in any sort of decapitating preemptive strike. That it can't also stop a nuclear-powered torpedo is irrelevant; that's simply not what it's meant for. Other threats are/will be countered by other systems.