It's just a particular way of working that some designers use who aren't concerned with the different requirements of different types of production or with anyone being able to easily edit what they've setup.
They can make a job setup more difficult to understand and they can also throw off the size readings in some applications.
If one is just printing, they usually don't present a problem other than sizing. For vinyl cutting, often the best approach is just to unmask and then delete the masking vectors. In other situations, converting them to a raster image is the easiest solution.