They didn’t use a hypersonic missile because they had no other way to hit a weapons bunker. They used it with a conventional payload to send a larger message. It fell on deaf ears.
Kinzhal has both conventional and nuclear payload capability. They sure did use use one and we know for sure. It carries either an 1,100 lb. high explosive (used in this case) or a 150 KT thermonuclear warhead. The use of this shows that Putin will do whatever he believes merits the situation.