That clock hasn't actually been built yet and it wouldn't be useful for guiding nuclear missiles.

https://en.wikipedia.org/wiki/Nuclear_clock

I mean, than nucleus is much heavier and much smaller than electron, so it will be much less affected by external forces. We may see no difference between sea level and space based Thorium-229 clocks, or difference will be much smaller.

ICBMs can be aimed as accurately as they need to be with current inertial navigation technology.