I also lived there for some time and while walking at night I usually noticed that most neighbourhoods were so much quiet and darker compared from what I was used. About pets and rodents I've never seen a stray dog in Tokyo or other places that I've visited in Japan, but yes I've seen rodents there also. I have a scary memory from the first time that I saw a weasel walking in front of me on a night walk because I was wondering "is that a cat? a dog? what is that?"