My guess is that it's programming doesn't just eliminate secondary effects, but all other effects besides dealing damage on the affected moves. It's subtle enough that this hidden glitch likely didn't show up in playtesting, and as a cartridge type thing Gamefreak can't patch it. In short, sheer force moves deal damage and nothing else, as the same programming that cancels the secondary effects also removes the hidden effects every other move and ability has, like say, activating colour change. Items that boost ally damage still work, though, and i'm not sure if rocky helmet hurts sheer force 'mon or not so while it could be deliberate, the scale and pattern of it's effects suggest it's not.
Basically, my moneys on a programming quirk that either went under the radar or is too tricky to correct, so Gamefreak went with it, thinking it not a big deal and/or interesting enough to keep. I guess whether it's tweaked/fixed in X&Y will answer how intentional it's effects are (or whether Gamefreak wanted to fix it, as an ability that ignores game mechanics in that way could require an overhaul just to fix one ability). But, yeah, my money's on a glitch.