There actually is a thread about mounting HDDs upside down. Many people chimed in and said "huh, my hard drive is upside down??"
As far as I know there is no problem with doing that. My hard drive is mounted upside down with no problems. But I haven't put it in the car yet. But functioning as a desktop, it works flawlessly.
EDIT: Since you said you did a search, here is a freebie. I won't blow the search whistle, but I just put in HDD upside down.
OK to mount hard drive upside down?