I was wondering what this would bring up. I have not heard of any ink formulations that are certain not to affect glass, though ink is often sold in glass bottles it tells you nothing.
I have seen glass marked with a technical pen using India Ink, but I would not be too sure that Indian ink will not etch the glass. Indian ink dries quickly but stays slightly raised from the service and is prone to chipping. I presume the above suggestion was for Chinagraph pencils, which are wax crayons in a stick. But would smear at a touch. Probably the best option is either the CD marking pens, special formulation of ink that does NOT etch plastic, or enamel paint applied with an ultrafine lettering brush, allows you to also use colour coding.
Perhaps... you know a friendly chemist who could apply some theory.