1
We went to Kyoto, where is one of the nicest cities in Japan.
We went to Kyoto, which is one of the nicest cities in Japan.
In relative clauses about places, use which when the verb after it tells us something about the place itself: ‘Kyoto, which is in Japan, is a beautiful city.’
Use where when it means ‘in that place’: ‘We went to Kyoto, where we visited some temples.’
2
I wanted to visit Bologna, where I had some friends there.
I wanted to visit Bologna, where I had some friends.
Where already means ‘in that place’, so do not also use there. We can say ‘I had some friends there’ or ‘Bologna, where I had some friends’, but not ‘Bologna, where I had some friends there’.