I never actually understood the whole Kuro theory but I think that ever since Shiro went missing at the end of season 2, and then they found him again. I think that the Shiro they found is actually Kuro because in S5 E3 when the paladins went to that mind void thing, Lance heard Shiro call out to him, but he didn't hear what he said. And then when he asked Shiro about it, he says that he didn't say anything. Also he shouted at Lance for no good reason. #NotTheRealShiro Plus Black didn't trust Shiro after they found him for a while.

So, I think that just before the real Shiro got blasted by Zarkon in S2 E13, Black sort of absorbed him into herself to protect him from the blast. That also explains why his body wasn't inside the Black Lion when Keith went inside to see if Shiro was okay. But since his body wasn't there, it's safe to assume that Black had something to do with his disappearance.

That also explains why Shiro escaped so easily from the Galra base. The Galra probably wanted him to escape so that they could find him and thus, use Kuro as their eyes and ears. That's why the Galra knew just where Voltron was almost all of the time.

I'm not really sure if this is correct or not because it seems a little far fetched. But, it's what theories are for, right? You collect and analyse information then put them together to create a simple (or not so simple) explanation, and not knowing if you're right until the time comes.