I've seen them censor when there's nothing underneath that even needs to be censored. I swear they do it because they like it that way (to hell with the excuses blaming it on the law! ^_^)
I think it's an err on the side of caution thing. Why take the trouble to knock out just the naughty bits when you can slam a bubble of pixelation over both parties' entire pelvic regions? At least they're sure they covered what they needed to.
It makes me wonder what the penalties for uncensored porn in Japan really are.
i think there's some jail time involved if it's not followed. i remember hearing an artist got arrested for such a thing a few years back because he didn't censor his h-manga.