I expect Real to recall Reinier in the summer and loan him out somewhere else. Dortmund has better options like Reyna, Reus, Brant, etc, so there's a reason why he wasn't playing.
Kubo isn't a right fit under Emery. Emery isn't afraid of using young players, but if they have flaws that are big enough to mess with what he's doing he won't start them. From what people say of Kubo, he's not been bad but not good enough off the ball for what Emery wants.