Same reason they aren't effective against jet aircraft. The bullets don't have enough momentum to keep going straight in their trajectory, hit the fuselage, penetrate and do damage inside. Instead, as soon as they are caught in the missile's flow field, they are swept along with it.

The only way CIWs can be effective is if you shoot them from particular angles (i.e. facing the front of the missile primarily), from a close distance (meaning the missile might still pose a danger even if destroyed/damaged), and if you use a lot of them simultaneously to create a wall of bullets where some will hopefully damage the missile in a critical way, as the missile's path passes through them.

Otherwise, you need to hope that whatever is coming at your CIW, is going to slow down and fly low and straight before impact, so the bullets can actually have a chance of penetrating its flow field. But that's not something that hypersonic missiles do. Instead they use their last stage to get even faster, and approach the target vertically from high above.