vacuous is mostly historical.
Back in the day it used to be implemented by an unsafeCoerce at the behest of Conor McBride who didn't want to pay for traversing the whole Functor and replacing its contents, when the types tell us that it shouldn't have any. This is correct if applied to a proper Functor, but subvertible in the presence of GADTs.
Now the Data.Void.Unsafe module provides that functionality (as unsafeVacuous) and vacuous itself is provided for compatibility with code that used it, and is left in case we ever get something in Functor that lets us apply newtype coercions directly to the Functor's parameter.