The motif for the line are Yamata no Orochi (mythical Japanese serpent with 8 heads), but actually giving it so many heads made it a little displeasing so they gave Hydreigon one real head, and made its arms and wings look like it had many heads when in silhouette.
The heads of Hydreigons are really hands and do not hold even the slightest bit of individual brain power.
I've seen this in two different places, but no source for the interview.
Regardless, Hydreigon has only one brain, so you still have to wonder where the other one went, and what it's like to suddenly sprout a second head, then have it disappear.