I never even considered there might be a problem putting them in upside down or something. Think the screw holes on HDDs and bays steer you to putting them in silver side up somehow, but I don't really know..
Looking at my Antec p182 I think I can confirm it doesn't matter - the case is laid out so the four HDDs in the bottom tray are oriented perpendicular to the two in the middle tray. So however the case is oriented, a minimum of two HDDs will not be 'upright', and they wouldn't have done that if it mattered.