Say if someone said "Why did you call him Japanese?" and then I said "Well, he IS Japanese (after all)." How would I express this? I'm thinking I would say something like this:
彼は日本人なんだ
But I'm wondering if using んだ/んです is the best way to emphasise exactly what I want to be emphasised in this instance.
Most commonly, we would say:
・「だって日本人（なん）だもん。」
・「だって日本人だから（だよ）。」
・「なぜって（or なんでって）日本人だからです（よ）。」
Notice a 「んだ」 is used in the first sentence.
The vast majority of native speakers would not use a pronoun like 「彼は」. They might use 「あの人は」, but it is not needed as both parties know exactly who they are talking about.
Since Japanese is a highly contextual language as I say here every week, the exact phrasing of the answer depends heavily on how the question "Why did you call him Japanese?" was asked in Japanese.
If you used 「なぜ」, the other person is likely to reply with 「なぜって」. Similarly, a 「なんで」 question is likely to be replied with 「なんでって」.
In informal/若者語 speech, you could also say
日本人だもんね
Which exactly corresponds to "he is Japanese, after all" in English.
