Last edit: 16:19, 26 January 2016
You're both right, that modern Japanese uses affirmative words for the purposes mentioned, but it is still the case that the words have affirmative meanings. Moreover, I'm interested in traditional meaning over innovated meaning; しかり was used in the past despite its modern disuse, and 応 (おう) is a Sino-Japanese borrowing, which may have never been directly used to affirm statements, but which nevertheless holds the meaning of affirmation which seems to be lacking in any form in Proto-Indo-European.
What source are you getting 応 (ō) from as an affirmative reply? The closest I can find is ōzu (Sinic ō + verbalizing suffix zu; evolving into ōzuru and thence modern ōjiru) as a verb meaning "to reply, to respond; to follow along in accordance with changes; to respond to events; to follow an order or request". The closest sense to "reply" is clearly the first, but that could just as easily be a negative reply. The closest sense to "affirmative yes" is the last, and that one doesn't necessarily have to do with speaking.
There *is* plain-old native Old Japanese おお (ō) that's used as a synonym for はい (hai), i.e. sometimes in a sense of "affirmative yes" and sometimes just as "I hear you, uh-huh". It's also used like "huh" when one just thought of something; or like "hey" when calling after or addressing someone; or like "oh!" as a surprise noise; or like "oh, oh, oooh" as rhythm sounds in poetry or song; or like "ooohhhh" as a groan.
In addition, if you're into etymologies, it looks like 然り (shikari) evolved from しか (shika, “just, only”) + あり (ari, from aru "to be (inanimate)"), literally "just (as it) is", i.e. "it is so, it is thus", more in line with affirmative-term trends other languages.
応 is listed under "Synonyms" in the entry for はい. I'm a little skeptical of your etymology for 然り. Where did you get it?
Re: 応, such use of the kanji would likely have been ateji for native OJP-derived おお (ō). The only usage I can find of it is in the set phrases 否も応もない (ina mo ō mo nai) or 否でも応でも (ina de mo ō de mo), both essentially meaning "whether one disagrees or agrees", i.e. "to have no choice".
Re: 然り (shikari):
Ok. I was under the impression that the original kanji 応 as borrowed carried a meaning of "agree", though.
Yeah, it's a bit fuzzy. Shogakukan's entry defs in JA say basically that it means primarily "reply, respond", but with a meaning of "agree" in there too for the set phase 否も応もない (ina mo ō mo nai); Daijirin's entry lists 承知 (shōchi, “know; understand; consent or agree to something; permit, allow”) as a synonym. It's also used in 呼応 (koō, “call, hail; agree with (as in grammatical agreement); in cooperation, in concert”).
Hearkening back to your initial question about affirmatives, I think Japanese はい (hai), うん, and おお (ō) come closest to meaning plain-old "yes", with the caveat that they also mean other things depending on the context. Then again, Shogakukan's pretty good about including the oldest quote for first usage, and I don't see the Kojiki or Man'yōshū listed (and I'm not familiar with most of the more-recent titles shown, but quick checks suggest they're from kabuki plays or other monogatari), so these might not be old enough to meet your criteria.
Does that help?
Yeah, I think I have a better understanding now. So, in terms of etymology, I would guess that うん and おお developed out of onomatopoeia. Do you have any more insight about the etymology of はい?
I don't have much. The Kokugo Dai Jiten quotes for early usage don't date any further back than the late 1700s, while Daijirin doesn't give usage quotes, just usexes; same for Daijisen. None gives any etym.
The etym in the JA WT entry at ja:はい suggests a borrowing either from Cantonese 係 (hai6, “yes; it is, there is”) or from Mandarin 拝 (bài, “to kowtow; to worship; to salute; to pay respect”). The Cantonese term could be viewed as similar to other languages' versions of "it is so," while the Mandarin term could be seen perhaps as "I acquiesce, I go along with what you say."
I'm intrigued by how late this borrowing might be, judging from the late date of quotes in the KDJ, and I wonder at how that might have happened -- perhaps something in the popular media helped spread the term? No real idea.