They’re aerodynamically stable at hypersonic speeds, and they re-enter the atmosphere so fast that after they’re released from the upper bus (which is itself a liquid-fuelled rocket powered spacecraft that can manouver and orient everything correctly before releasing each individual MIRV) the amount of time they actually spend in the atmosphere, and thus the amount they get deflected, is both trivial and very easy to correct. It’s basically like throwing a dart accurately at that point.
Bear in mind that modern MIRV’s, quite unlike normal reentry vehicles such as the space shuttle, are specifically designed NOT to be blunt-body, which means they actually do not slow down all that much as they go through the atmosphere. This makes them get amazingly, incredibly hot, but they’re designed to hack that.
Manouverable vehicles like MARVs and hypersonic glide vehicles are a bit different
Paraphrasing the wikipedia article, the final missile stage itself picks the first trajectory, ejects the first warhead, then shifts to the second trajectory and ejects the second warhead. It iterates through each trajectory, dropping each warhead as it goes until it completes its full barrage.
Worth note is that not all of them will work the same, and some designs may include aerodynamic guidance or individual rocket motors.
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