Since the ninja is a Rogue sub class it should be elligble to take other rogue alternate class features which replace existing class features such as scout, which replaces uncanny dodge/Imp. uncanny dodge?
An Alt class is an archetype. So he can take it as long as they do not exchange the same abilities. As scout replaces uncanny dodge, something the ninja already replaced, no he can not have both.
Most archetypes replace things the ninja has replaced {like trapfinding} so mixing and matching is hard.
Ninja HAS uncanny dodge.
Oops you are right, not sure why I thought it was swapped. In that case yes, scout can be used as it switches nothing else.