I could be wrong but I think you could have both classes because one is more of a thief and the other more of an assassin. The class is a full class so this also is another reason why you can have both. Barbarians and Rangers are in truth just alternate fighter classes but you can use those together. In addition, with archetypes for rogues you could make the rogue class very different from a ninja. Imagine mixing ninja, Rogue (investigator archetype) and perhaps master spy.
However this does feel a little on the grey side so it might be your GM's call in the end.
Ninja is an alternate class for the rogue. Like a big, in-depth archetype. It's not really "Ninja" and more like "Rogue(Ninja alternate)". So Tilquinith is right, you can't take levels of both.