It is perfectly possible that N's parents turned him over to Ghetsis willingly without them dying and without Ghetsis being the real father or a relative of N. If Ghetsis is a "king" or government official, it is perfectly possible that N was turned over to him to become the ward of the state for whatever reason.
I like the idea mentioned by a previous post that N is a high level autistic. Autism is the inability to "filter" sensory information, especially as is necessary to understand social cues. It is possible for someone like that to pick up on things that others don't, making it possible to understand the mood of pokemon if not a basic communication structure.
Since N is still has the instinct to be social and since pokemon communication and moods are more simple and straightforward, N could be more comfortable around pokemon than he is around people. That could be why he lives in the woods. It is fitting given that satoshi tajiri, the creator of pokemon, is a high level autistic who spent his childhood collecting insects in the forest.
In literature, there is something called the "unreliable narrator." It means that you can't necessarily trust what you hear from the narrator, and the narrator typically doesn't tell you himself that he is unreliable. For instance, N might not be an orphan or might have "orphaned" himself by declaring that his parents were "dead to him."
N could "communicate" with pokemon by knowing what they are feeling because a lot of communication is non-verbal. As for a higher level of communication, I am skeptical. A lot doesn't fit right regarding N. He should NOT have learned anything earth shattering from his battles with you.
If he can have high level conversation with a pokemon, some pokemon at some point would have had to say: "some humans are not that bad," even if the pokemon had simply observed nice humans without being owned by one. The other possibility is that you are the only or one of a very small number of trainers who are actually nice to pokemon in the pokemon world and that is why no pokemon that N has spoken to has ever known a nice trainer.
If your character is quite literally the only person in the game that doesn't abuse pokemon, N should recognize for the unusual exception that you are and continued to believe what he had believed about trainers other than you. After all, he spent his entire life having conversations with pokemon and never ran across a pokemon who knew a person like you.
Also, why didn't he know what Ghetsis was about if he could literally have conversations with pokemon? Some pokemon owned by the evil team would have communicated to N at some point that Ghetsis himself abused pokemon on a regular basis.
Regardless of the exact scenario, little should genuinely surprise N about pokemon-human relations if he can genuinely have a full conversation with a pokemon.
N might also be mistaken about how easily he can communicate with pokemon. For one, there are not unbiased independent observers who also understand pokemon and can "grade him" on how accurate he is. I am also reminded of my cousin (who isn't autistic). She used to think (and may still think) that she has a particularly strong bond with animals and could communicate with them. Maybe she does have an extra strong bond, but she overestimated its strength. One time, we rented horses to ride, and she started whispering to her horse. This made the horse very nervous. She sensed that the horse was nervous and whispered reassurance. I am certain the horse was nervous because it knew she was talking to it but not loudly enough for the horse to hear any of the words. (Horses like a lot of domestic animals can recognize individual words even if they can't understand a sentence.) Also, the horse was probably nervous because my cousin was doing something he was not used to.
