I'm not saying it's as good as fans, but the SilentDrive (or whatever it is) enclosures has a large metal plate that presses against the top of the drive and one that presses against the bottom. These plates are the same pieces of metal that attach to the main case of the computer, so it should do a reasonable job of transferring heat. So it's not like they're not being cooled at all. I'm sure that it would be better than your stacked drive example, but obviously not ideal from a cooling perspective.

Personally, I have one drive that's way louder than my others, and I've been thinking about getting just one of these to house that drive.