The sound waves aren't only vibrations and energy. They contain some sort of spiritual attack that is wearing down their soul. It also contains an element of illusion that is reducing their resistance.
It is a combination attack in a single move. The illusion is weakening their will to fight while the other physical and spiritual attacks battered them nonstop.
The Stellos are worse than those who were flaking away as the sound waves battered them. The scream struck them and they shattered directly without any resistance. This is just because of the physical vibrations from the sound.
Earth is weak to sound after all. The Stellos have a high resistance to physical attacks but the sound waves are at a frequency that enables them to bypass the potent defense of the Stellos.