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Unfortunately, the Second is measured for purposes of our timekeeping standards at sea-level on Earth which is ~1PPB slower than it would be in free space, as opposed to having a correction factor built into our time standards and so, for example, interplanetary ping times would be slightly shorter (in UTC/TIA nanoseconds) than expected.

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A much more precious clock is used by USA to guide nuclear missiles without GPS. (nucleus of Thorium 229 controlled by a high-precision UV laser?)

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.

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