Here is another rebuttal to some of the statistics cited from self-report online surveys in the original Guardian article. I don't know how reliable the data on frequency of sex in this rebuttal piece is either, but there are some interesting and pertinent observations under "Mistake 5" and the section "So, What Was the Real Problem?"
http://www.yutaaoki.com/blog/top5-mistakes-journalists-make-about-sexless-japan
Having lived in Japan for a year and a half, I found the sexual attitudes there all over the map, from rather pronounced lack of interest in sex to a fair amount of overindulgence in sex. The urban centers in particular have quite overtly sexualized cultures. There are certainly people who have various kinds of sexual phobias there, as the original Guardian article showed, but I see no reason to believe that this is either unique to Japan or responsible in any significant way for other issues that are more major. Two of them do seem to be the interrelated problems of the ominous and looming consequences of the low birth rate and the increasing reluctance of young people, many women but slowly increasing numbers of young and often alienated men too, to marry (somewhere between one in six to seven Japanese women now never marry). There are complex reasons for that which I doubt can be reduced or attributed to any one overriding factor, but gender issues, more often of modern than traditional forms, and how these play out in terms of a number of economic and social incentives, certainly should rank highly in any reasonable assessment.