1. Radar has to scan more frequently to track a hypersonic.

2. Because they can change course at high speed, a slower intercept weapon will miss if it counts on predicting the flight path to intercept. At present this is how most surface to air and point defense weapons systems work.

3. Point defense systems may not be able to react fast enough to stop a hypersonic.

4. More kinetic damage. This is significant for ships.

You can't intercept them (yet) and they're difficult to detect. You don't see that as an advantage for standoff weapons?

The SM-6 has some limited ability to intercept hypersonic weapons. This hasn't been tested in a realistic way yet.

https://seapowermagazine.org/vice-adm-hill-mda-pushes-space-...