I think the comment by the expert government advisor is probably correct: the confirmed cases are just the tip of the iceberg. However, I had some unrelated tests to do at a hospital in Shizuoka prefecture and had to stay overnight. I asked the nurses what they thought and if they had seen anything unusual in the past month. Although there are about 60 confirmed cases in the prefecture, in the hospital where I was staying Corona virus seems not to have touched it. Obviously anecdotal evidence, but the nurses claimed that everything was business as usual and there was not an increase in respitory illnesses, etc.
I really do fear golden week, though. The news has been full of coverage of people going to places like Kamakura, filling up car parks and creating traffic jams. After being fairly severely rebuked by both the government and the media, I've heard that people are mostly taking it seriously, but we'll see starting tomorrow I guess.