I'm probably being incredibly naive in saying this, but what about "non-wartime" decapitation strikes — where instead of going to war, you just lob some well-timed hypersonic missiles at your enemy's capitol building / parliament / etc. while all key players are inside; presumably not as a way to leave the enemy nation leaderless, but rather to aid an insurgent faction that favors you to take advantage of the chaos to grab power? I.e., why doesn't the CIA bring ICBMs along to their staged coups?
A key advantage of a hypersonic weapon is the possibility of first-strikes to disable the enemy's retaliation systems before they have the ability to launch more-traditional retaliatory responses. Only submarines are likely to be mostly-immune to them.
https://www.heritage.org/asia/commentary/chinas-new-weapon-j...
There are counters to hypersonic glide weapons beyond shooting them down. If you can detect it early enough then the target ship can change course and try to evade. The sensors on those missiles have very limited field of view so if it's not receiving a real time target track data link for course correction then it can be possibly be dodged (depending on how many are incoming, weather, and other factors). Even if the target can't evade, a bit of advance warning would at least allow for cueing EW countermeasures.
I supposed the point would be to hit the highest priority targets and nothing else. Loss of command and logistics has a profound effect on endurance