I read a similar article (i suppose it cited this wired article) on Ars Technica this morning. Although it tries to frame the site as some sort of right-wing terrorist incubator, I still found it interesting that the imageboard is owned by a toy company. I don't think these imageboards are or will ever be profitable to operate. If I had to guess, they're funded out of pocket by the likes of "hiromoot" or the owner of this toy company.
I really doubt that this japanese toy company is the one pulling the strings behind these terrorist attacks.