In my /Library directory I have two folders of fonts - Fonts, and Fonts Disabled. Would deleting the Fonts Disabled folder cause any issues?
If you're currently having no problems without those fonts, actually deleting them should not cause any problems. The system just ignores the fonts in the folder "Fonts Disabled" so there should be no effect on the system.
Just be careful you don't delete the following fonts:
located in /System/Library/Fonts. These fonts are used by the system. See also http://www.macworld.com/article/1051630/tcofonts.html