I could be wrong but...
I think the crystals hit right as the red circles appear for where they hit.
This makes it difficult to dodge that attack.
I could be confusing it with the super-long-range stomp attack.
Do the crystals actually hit when the red circles appear (as opposed to complete, like bombs)?
No; think of it like this.
Crystals soars through sky, and hits the ground. The impact is larger than the actual crystal, so it looks like it's invisibly hitting you, when it's probably a glitchy explosion or something. The red circle shows the full impact radius, and the crystal itself inflicts the Shock status.