I have tried it, mounting the fan under HDD as exhaust makes the bottom of the box and the HDD red hot, and mounting it as an intake fan(the way it needs to be mounted) under HDD the top of the box gets just as hot as with no fan, because the aperture is far too small.

Obviously you have you fan exhausting hot air downward(hot air rises) it is keeping the top of you box cool and you're happy, thats fine but common sense tells you it isnt actually helping...