Never heard of HDD's facing heating problems.
SATA ports are known for me to fail because of moisture and cheap cables only.
Otherwise it could be voltage regulations because of the PSU, mobo or the HDD's itself.
As for ventilation; typically it is pusher fans to the part then puller fans on the chassis and the current has to circulate. It's different for cars, tho, since driving will cause air to hit the grills so it's better to use puller fans