It's because atan2, along with all the other inverse trigonometric functions, is incredibly slow. On a GPU, sin and cos may be a couple of cycles, but asin/acos/atan/atan2 may be upwards of 30 or 40.
Often times, angles are best avoided when possible for this reason. Normalized vectors end up faster and simpler in many cases.
Relevant anecdote: I recently wrote some code to compute normals in 2D and thought I would be clever by encoding the normal as an angle to save space. It turned out that the atan2 call at the end was so slow that it outweighed the cost of everything else I was doing several times over. Lesson learned…