From a quick crash course of youtube tutorials, I've found that alcohol inks can be used on non-porous material like glass, metal, and acetate/transparencies - which is what I'm going to try out. You mix drops of ink with an alcohol solution (or just rubbing alcohol, it seems). This tutorial gives a pretty good overview and covers what i think could be adapted for shadow puppetry design.
http://www.youtube.com/watch?v=rQp6_GkNsKoI wouldn't be using as much ink; I'd just aim for an "ink-wash" so hopefully light would still pass through it and maybe try to create some sky/seascapes, or just to add some accents of colour where I'd otherwise use cellophane or similar. It'll probably take a bit of trial and error to get right, but I reckon it's worth experimenting with.