In general, if your visit to Japan coincide with Japanese holidays then it is possible that there will be some lines at museums, temples, and other tourist places. Any other time there should be minimal line at tourist places, especially on weekdays.

Your travel is in October and if visit coincide with foliage season then those foliage locations can be busy, but during October there is no major Japanese holidays. Only Japanese holiday in October is 10th. Beside foliage locations October tends to be low season for tourism in Japan.