Nguyen is a Vietnamese surname. A bit of research shows that it comes from 阮, and the same character in Mandarin Chinese is pronounced 'Ruan', and it's different in other Chinese languages. I'm not sure if it's a surname in Japanese though.
If you're having a character with the surname Nguyen, I think you'd expect them to at least be of Vietnamese descent. If you're designing a Japanese or Chinese character, why not use a Chinese or Japanese name?