Sorry if I am being too simplistic with the question. I mean, whether in comprehensive character dictionaries like Dai Kan-Wa Jiten or modern applications like Kanji Study, when there are “obsolete” pronunciations kun’yomi or on’yomi, do they refer to Classical Japanese?
I mean (and referring both to common or obsolete pronunciations) can the pronunciations of the kanji in the classical japanese texts from the Heian period to the 19th century be consulted in any modern comprehensive kanji dictionary or are we talking about a matter that requires lexicons specialized in lexicography and paleography of a specific period of the language?
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Can you provide some examples of such entries? It’s a bit hard to understand what’s going on without actually seeing what you’re seeing.
Japanese will have been pronounced many different ways over its existence but when old words are read by modern people, they generally use modern pronunciations: きょう for けふ and so on. The historical spellings you see in dictionaries were actually in use until post-WW2 spelling reforms, too, and even before the spelling changed they’d used their modern pronunciations for a while.