Why does Latin not have an emphatic yes or no?
Who can say? They certainly don't have the exact words, but you can put together emphatic ways of saying yes and no. For example, yes: sane, etiam, ita. No: non ita, non vero, minime.
You can, as I'm sure you're aware, simply answer questions like "Can you cook?" with "I can". Some scholars in the Middle ages were also perplexed by this "defect" in Latin. Peter Abelard in 1121 wrote a philosophical treatise called Sic et Non
(thus and not), attempting to put together a simple affirmative and negative in a language which didn't possess it.
However, Vulgar Latin, or some later period of common speech, might have had these words, but since the words for yes vary quite a bit in Romance languages the words probably developed after the colonization of these areas. There's the langue d'oc
in the south of France, the langue d'oil
in the north (oil, which should have an umlaut or diaresis or whatever over the i, later became oui), and the langue de si
Quis ab bello contra Iraqem non mutatus est? aut bello ullo?
Agimus de tales res hic