The atmosphere has nothing to do with it.Why would there be any Coriolis effect once you're out of the atmosphere?There's going to be a minuscule variation in direction due to the changing angular momentum as your missile gets closer to the pole, and a countervailing minuscule variation as it gets closer to the equator, having passed the pole.
For an object as small and fast as a ballistic missile, that variation would be truly tiny, but it's going to be present in any launch not exactly parallel to the equator.
It's a conservation of angular momentum effect.
But once you're clear of the atmosphere how does the Earth's rotation have any effect on the missile? The velocity of the launch platform simply becomes one component of the missile's orbit. (And, yes, it's an orbit--it's just the periapsis is below the surface.)