To my best knowledge -- which, as far as InDesign Server is concerned, is *zero* -- InDesign uses all of the locally installed fonts, the ones in Adobe/Common/Fonts (not sure about that path), and the ones in InDesign/Fonts. These paths are hardcoded, there are no preferences or settings to change.
Of course it may differ for ID Server, but a random search through its DOM does not reveal anything about font paths. So if it's there, it's not scriptable.
Have your tried asking on the ID Server forum?
(One of the things I wanted to try, jus' for laffs, is to see what happens if you put a *link* to a font file in one of the font folders. And what if the link points to a folder instead? Ah, but I'm too busy with Real World Work, no time to experiment...)