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I do for duplicates, and the names "Swahili", (I think that having a villager named after a language that I'm learning is a bit too comical) and "Konichua" (it's spelled "konichi wa"). They get replaced with Swahili names, like Hatima (destiny).
Sometimes, I name villagers after a parent ([Name] II).
I also change the names of the people who dislike running to [space], as they don't deserve names. >:O