>>31417933N's character is based around his ideals. In his pursuit of his ideals, he encounters truth that challenges his beliefs. He believes that humans and Pokemon should separate, but throughout his journey, through not just the protagonist, but everyone he meets, he sees humans and Pokemon living together happily. And hes not blind to this. He notices this, as his end of game dialogue shows. A good example is in BW2, he talks about how he hates Pokeballs, but the Pokemon that he releases actually seem sad when he does.
But he continues anyway.
Furthermore, N, as part of Ghetsis's plan, has never even known the truth. He was shown only what Ghetsis wanted him to see. All in order to shape his ideals.
This is one of the reasons that he wants the protagonist to get Reshiram, the Dragon of Truth. He wants to prove that his ideals can overcome the truth. That his ideals can create the truth.
But the truth is not objective. The truth is just that, the truth. And it is through the protagonist using the truth that he is able to finally accept it, and he grows.
The dragons are a fantastic metaphor for the plot.