(At least if you’re ever needing to compose rotations; to apply a quaternion to a big array of 3-vectors, go ahead and convert it to a 3x3 matrix first, which should end up slightly more efficient.)
3x3 rotation matrices are really hard to keep normalized properly, whereas quaternions are trivial to normalize (just divide by the norm).
If you need to compress a unit quaternion down to 3 numbers, instead of taking the logarithm (which is computationally expensive and a pain to deal with) use the stereographic projection.