DoubleTap-
As I recall, there has never been a way to hide drives from showing up in Defraggler. Unfortunately, the latest release doesn't seem to solve this problem either. A good talking point in the Suggestions thread, perhaps?
Of course, I could be wrong. If there are more experienced users who can point me in the right direction, I would love to know how to fix this. I've used Defraggler for about 12 months now, but I can't ever remember being able make that kind of change. It's certainly a good talking point, though!