I don't really agree with your assessment, though I really only know about Japanese culture from the last 10 years (when I moved here).

There are really 2 main differences between American and Japanese culture with respect to otaku/nerd culture and being bullied. First, Japan high schools are very highly streamed. You pretty much know what you are going to do in life when you apply for entrance to high school. High academic achievers will go to a high level high school, go on to university and then go into white collar jobs. Low academic achievers will go to a low level school and from there either go to a trade school or go out straight to work.

So, the "nerd" culture doesn't really exist in high school. You are either studying your ass off in a school that is overloading you with academic work, or you are enjoying sports or some other club activities and barely ever study. Bullying obviously exists, but it's not around academic boundaries. The "smart" kids aren't bullied for being smart. In a low level school, there are thugs that are turning you upside down for your lunch money. In a high level school, there are the rich kids who look down on you. But being smart is pretty much 100% a good thing in a high level school. If you are smart in a low level school, then you are an underachiever and probably cool as hell, so everyone loves you.

Otaku culture is something very different in Japan. It's more that you like something that is not cool. So maybe you like comic books too much. Or you are obsessed with games. Or maybe you collect stuffed animals. Or whatever. But basically it's something that your are passionate about but absolutely embarrassed to tell anyone. Nobody admits to being otaku in real life. It's practically a swear word.

Hikikomori is completely different than otaku. I have an internet friend who is hikikomori. He just has intense social phobias. It's a mental illness. In Japan, although it is getting better these days, mental illness was not treated. Like, seriously, no treatment. You are looked after by your parents. So if you have schizophrenia, your parents look after you. If you have clinical depression, your parents look after you. This is also true of other kinds of handicaps like Downs syndrome. Parents look after their children if they are not able to look after themselves.

A lot of hikikomori could probably lead productive lives if they got some treatment for their mental illness and slowly awareness is improving. But this is hampered by Japanese culture of not understanding mental illness. It's doubly hampered by the feeling of duty that parents have towards their children (which is admirable, but unfortunate in this circumstance). People feel that it is their responsibility to deal with the problem and they won't go to get help.

There are people in the west with the same mental illnesses that hikikomori deal with in Japan. The difference (as another poster mentioned) is that western parents will not look after their children in the same manner. There is more of an attitude that somebody else should do something to help them. It's one of the things I hate most about Western culture, but in this instance, it's probably the exactly right thing to do ;-)