It depends. For composing multiple transforms, composing versors aka quaternions/dual quaternions is cheaper than a full 4x4 multiply. For a single application, a 4x4 will be cheaper.
Quaternions are used in animation for blending and composing transforms for a reason. You don't have to trust me, but yes... tried for maybe ten years and counting from doing graphics and animation work.
> If the quaternion is used to rotate several points (>1) then it is much more efficient to first convert it to a 3x3 Matrix. Comparison of the operation cost for n transformations:
> - Quaternion2: 30n
> - Via a Matrix3: 24 + 15n
So really it depends on what you're doing (admittedly here it is 3x3 not 4x4)