As a general rule, the places oriented towards tourism do not close on public holidays for the most obvious reason (National Museums tend to close on the next day, but the ones you cite are small-scale private or local government sponsored ones).
Kyoto's most popular sites like Kiyomizudera, Kinkakuji, and Fushimi Inari are rather busy on any day.Edited: 16 November 2016, 20:10
One more question, I read somewhere that some shops in Kyoto close on Wednesday. Is it correct?
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