Pretty sure subclasses can’t take their base class’s archetype. But even if they could, this still wouldn’t work, because the ninja has no trap sense to trade out.
|
Alternate classes are standalone classes whose basic ideas are very close to established base classes, yet whose required alterations would be too expansive for an archetype. An alternate class operates exactly as a base class, save that a character who takes a level in an alternate class can never take a level in its associated class—a samurai cannot also be a cavalier, and vice versa.
According to this, there's nothing in general preventing Ninja from taking Rogue archetypes. But, as Melkiador points out, you don't have the right ability to trade out.