New Years is a time when most Japanese people go home to their families - all businesses, stores. museums etc. close down.
There are several threads on this forum with suggestions for people who visit during those special days. It can be quite entertaining to visit shrines and see ordinary Japanese people paying their respects etc.. But if you're feeling at all fragile, it might be a little depressing to arrive during the end-of-year shut down. (Imagine coming from another country to, say, Boston during the Thanksgiving holiday).
Things will start to return to normality from Jan 3 or 4.