The cultural norm definitely helped with covid. But that cultural norm you gave just doesn't exist. A more realistic cultural norm here in Japan is avoiding confrontation, and it seems a lot more likely that just wearing a mask so you don't have to have a confrontation with a convenience store employee is more likely than some grand honor and respect culture that has no basis in reality. Just a romantic vision of the country that began in the early 20th century and lingers still.
That said, the obvious caveat that culture isn't consistent and can't explain everyone's behavior is necessary. There was anti-mask and anti-vaxx protests here last week on NYE. They were harassing people at Comiket because Comiket required vaccination cards and shit.
The skeptical attitude pre-dates the more recent Western “anti-vax” sentiment that has thrived on social media, with its roots instead in past vaccine-linked events and legal rulings that encouraged the government to take a passive stance on vaccination.
And ironically, Japan’s relative success in handling the pandemic means an urgent rollout of the shot is less of a priority. The country has avoided a second state of emergency, even as cases have increased to record levels.