I’ve only seen through season two, but I don’t see them as being particularly naive. At least, not more so than the rest of the cast, who can be pretty fucking stupid when the plot requires. Especially Peter. Hiro is an example of a stereotype (the “otaku,” or nerd) that exists within Japan, but I don’t think you can make a convincing argument that he’s supposed to be representative of Japanese people. This is contrasted by Ando, who doesn’t really care about comics or superheros, and thinks his friends is a bit nuts until about halfway through the first season. But both of them are pretty clearly portrayed as a pair of losers. That is to say, rather than be exemplars of their society, they are disconnected from and outside of it.
Actually, I should say that Hiro is originally very naive, but it’s an extension of his fundamental idealism. His initial reaction is to expect the best of people. By the second season, he’s still got that idealism, but has lost a lot of the naivete. Once Adam shows his true colors, he doesn’t waste too much time trying to redeem him again, and takes some pretty hard-core steps to neutralize him.