Yes, we are social animals, but for much of our evolution we were social in much, much smaller groups... even smaller than these 'sub' cultures the article is talking about. Hunter-gatherer societies only had around 10-50 people in each group; we have evolved to be social in groups of this size.
The 'hyper-specialization' that you speak of might be a way to get our group size back to this original size that we have evolved to be comfortable in; the huge, un-natural, size of popular culture might be what we are reacting against.
The hyper-specialization we're talking about is specifically a way to avoid having a social group. While the hikikomori may not have exclusive interests, the whole point is to avoid physical contact with anyone at all. Maaaaybe I just can't see far enough into the future, but personally I think physical contact with other people is still pretty important.
Also partaking in popular culture doesn't mean pulling everyone alive that's interested in that culture into your social group.
The 'hyper-specialization' that you speak of might be a way to get our group size back to this original size that we have evolved to be comfortable in; the huge, un-natural, size of popular culture might be what we are reacting against.