Also consider that pin point accuracy means that you can drop a second in the hole left by the first one. Assuming that you have plenty nukes to burn and a priority target like a bunch of highest level government officials hiding in an underground bunker.
I've seen the theory of pinpoint nukes lining up to bust open the deepest bunkers. Point blank, if you can hit a target with that many nukes, you basically already control that target. if you control that target, digging out the bunker is easy enough to do instead, and you can retain all of the intelligence that target inevitably contains.
I've never seen any news, intelligence, or even heard rumors from military friends or family, who include more than a few nuclear engineers and physicists that our government level bunkers are at any real risk, nor Russia's, for that matter.
The earthquake risk is real, but it's not controllable. Too much relies on large pockets of methane (natural gas) being present, and the detonation bringing in enough air to allow the spark to set up a chain reaction. It's not a predictable thing.
That means that there is a risk, of that you're correct, for even the deepest, most hardened bunkers. But it's not a high risk.