I'm not surprised the CSS property does not work (or <sub> for that matter). In-line bitmap images (e.g. of number glyphs) can't be hyperlinked from what I remember, either.
You could use various symbols like '+' or '*' instead of numerals, of course, including any of a number of 'special' Unicode characters (see http://kindleformatting.com/book/fil...Characters.pdf
for a 'starter' list). TTS will ignore these, though then you have to probably live with a list of citations whose labels cannot be located in the text (but these should have backlinks to take you to the reference in case you forget to use the Back button). Or you could use a citation style that includes a quote from the text that referenced it.
You might also check the KDP forums on Amazon.com to see if anyone there has other ideas.
But I would not worry about it that much, depending on the audience. Anyone who uses TTS enough will train themselves to ignore interjected numbers like this.