But even then, when he is really able to understand Pokemon (in the sense, he knows what they are talking) then he should also be able to listen to them when they tell him about how much good the humans also have been doing for Pokemon. The Pokemon Centers help EVERY Pokemon. Regardless if they are wild or from a trainer.
And he had more as once the chance to talk not only with Ash but also his Pokemon. And Ash alone is (in the later seasons) a really great friend to every Pokemon and treats them as friends.
What I actually try to get at is: After N learned Ghetsis lied to him about liberating the Pokemon, he still never questioned if he not maybe lied about other things as well. Like, not every human is cruel to Pokemon or treats them like dumb animals.