Neil's answer does not really deal with dialogue. Style manuals like the Chicago Manual of Style deal with academic and journalistic writing. If you want to apply them to narrative fiction, they only apply to that part of your writing that is explicitly in written language, that is, everything outside the dialogue. Dialogue is spoken language, or rather, dialogue in narrative fiction is the written emulation of spoken language, and it follows its own rules and styles.
To answer your question:
Dialogue is what people say. You do not say "9", but "nine". Therefore, in dialogue, you should write "nine".
This can become cumbersome to read, if long strings of numbers and/or letters are repeated often in dialogue. In this case the string becomes common and can be treated like common abbreviations (e.g. BMW or UK), which readers perceive as words and which therefore are represented in written dialogue in their word-form, not in their sound-form.
In your case your proofreader is right if that designation of a robot is said only once. If, like C3PO, it is used as a name-like handle to repeadedly talk about the robot, you should use the number-form instead.
If I was writing this story, my chaeacter would read M55/987.3 as: "fifty-five, nine eighty-seven, three".
My character wouldn't speak the slash and dot, in the same way an American saying a price does not say "three comma fifty". And he would not say the M either, because there is no 55/987.3 in any other series. You migjt say "three dollar fifty", but you need not, because it is the only currency in Ohio. If he'd have to refer to this robot often, he would call it "the fifty-five". That would serve as a name-like handle. He would only spell out the whole serial number if he was unfamiliar with the robot -- but then it would not be a name, because a name is a familiar word.
My character would say "fifty-five" in the same way that I don't say "Samsung Galaxy S III LTE I9305".