Are there any temples that are always empty?

No, but smaller sub-temples in the Daitoku-ji complex are significantly quieter than the main halls.

Is it worth buying a Kyoto bus pass?

If you are visiting three or more locations in one day, a 700 JPY one-day bus pass is a cost-effective way to get around.

How to visit Kyoto temples in peace

The only way to avoid the crowds in Kyoto is to start your day at 6:00 AM or prioritize temples that remain off the main tourist trail. Avoid the major sites like Fushimi Inari and Kinkaku-ji between 10:00 AM and 4:00 PM entirely.

Hit the 'Big Three' at dawn. Arrive at Fushimi Inari-taisha, Kiyomizu-dera, or Kinkaku-ji by 6:00 AM. Gates at many shrines are open 24/7, and you will have the pathways to yourself for at least 90 minutes before the tour buses arrive.
Choose peripheral locations. Swap the central Arashiyama sites for northern temples like Shisen-do or Enko-ji. These offer the same garden aesthetics without the heavy foot traffic found in the city center.
Follow the 'Golden Hour' rule. Most day-trippers from Osaka leave Kyoto by 5:00 PM. Visit your final temple of the day starting at 4:00 PM to catch the peaceful golden hour light just as the crowds thin out.
Avoid weekends and holidays. If your schedule allows, visit the most popular temples on Tuesday, Wednesday, or Thursday. Never visit a major temple during Japan’s 'Golden Week' (late April/early May) or Obon (mid-August).

Are there any temples that are always empty?: No, but smaller sub-temples in the Daitoku-ji complex are significantly quieter than the main halls.
Is it worth buying a Kyoto bus pass?: If you are visiting three or more locations in one day, a 700 JPY one-day bus pass is a cost-effective way to get around.