Nudist Beaches in Japan

「So there are no Nude beaches in Japan simply because it's illegal to be naked in public. Yet, why are there Nudist Beaches in Japanese Anime, and most locations within Japanese anime always occur in Japan?」
Speaking as someone who's watched a whole lot of anime over the past 30 years, nudist beaches aren't anywhere near common as a setting for anime scenes, at least anime that's not straight-up porn. Maybe "trip to a nudist beach" is showing up in some hentai anime you're watching, but then your question basically becomes "Why are things that aren't common or legal being shown in pornography?" which is a dichotomy that's not even remotely exclusive to Japan.

Anime is fiction. Think about that for a second before comparing to real life.