I know that languages, in general, can denote honorifics, especially with second person pronouns (T/V distinction, etc), and I imagine that the Japanese system of honorifics is probably an extension of that into other persons with more granularity. However, did the Japanese system evolve a thousand years ago? Two thousand? Are the honorifics derived from nouns or verbs or some other class of words?
As a partial answer, this dissertation by K. Russell reconstructs verbal morphology of proto-Japonic. Certain morphemes are reconstructed (ch. 4) at the level of proto-Japonic, but others are only reconstructed at a later level such as Old Japanese. The honorific morphemes -as-, -imas-, -tamap- is reconstructed to OJ. No honorific morphemes are reconstructed to proto-Japonic, although Ryukyuan languages have honorifics.