Ok, I have that exact Macally case on the desk in front of me at work with a previous-gen 1TB WD Green in it, and we've got one of the 2-drive versions of the Mercury Elite-AL Pro as well.
Both seem to have good ventilation, and the Macally case has good heat transfer as well, so I wouldn't feel uncomfortable about either unless you're going to be running the drive very hard, or very constantly. They'll both cool better convectively if you use the upright orientation, so it's probably worthwhile to do that.
I'm kind of curious, though: For a while, I was seeing the Macally drive occasionally hang completely, locking up all I/O on the Mac until you powered it off and back on (generating the "disk improperly disconnected" message, of course). Connected via FW400 to a PM G4 1000DP, then a previous-gen i7 iMac. It wasn't completely consistent, but seemed to happen about once a week (the computer is left on all the time and it does tri-weekly network backups to that external; no other access of it). The problem appeared to carry over to the iMac that replaced the old G4, but now it has apparently stopped--I haven't seen a hang in several weeks. Not sure if it was updating to 10.6.6 that did it, or if there was something else that changed.
Has anybody else seen this kind of behavior with that case?