I recon he was adopted. as were the people before him.
Think about it, N is a very disposable name. It seems very likely that there could have been a M and an L before him.
Guessing is useless. I find most of these stories to be too far-fetched to be considered "realistic," but if I just wanted to have a blind guess at it it'd be concordia or anthea.
That's a really interesting theory. Considering Ghetsis' attitude towards N, his nameplus who would want a kid with Ghetsis, it would make sense as far as the storyline if N never had a real mother.
But does that kind of technology exist in the Pokemon world? XD
N's mother is Wally's mother, and they are twins. She did not tell Ghetsis she was having twins, though, so when she had the first baby (N) Ghetsis only took him away. Wally's mom had him then and wen to Hoenn to escape Ghetsis's maniacal plans, thinking it was too late already to take N back from him.