Ah, hot springs. One of the finer parts of life in Japan. You should definitely experience one while you're there. While there can also be some very real experiences in culture shock while you're there, the onsen is absolutely worth adapting to the local culture.
Nudity: May as well get this one out of the way. Yeah, the overwhelming majority of hot springs involve nudity. This is why they're sex-segregated. There are non-nude places where co-ed groups of friends can go together. Still, nudity is the rule rather than the exception and for the most part you'll end up with old people who don't bother you.