The biggest factors that affect your player's temperature are the heater ducts in your car and how it's mounted in the dash. If there's space around the player, and the heater ducts don't run near it, it's gonna be cooler. The player will also tend to get hot if it's winter time and you're running the heater a lot.

The disk drive size won't affect the drive spindown. The bitrate of the music files might-- FLAC files would keep the thing spun up almost all the time. Having too many songs that your database is huge and takes up all the cache memory will affect the spindown, too. You can use the disk monitoring feature (it's in the emplode configure player screen) to see if the disks are spinning down.

If you only had the temp warning go off once, I wouldn't worry too much about a fan. If you tend to go on a lot of long drives and you've had the temp warning go off more than once, then I'd start to consider it. Stu at Eutronix can fix you up if you don't think you can do it yourself.