Here, "vaping" is a mistranslation. The law actually refers to 加熱式たばこ, or "heated tobacco products" (HTP), which contain tobacco leaf just like regular cigarettes, but don't combust. On the other hand, nicotine vapes are classified as medical devices and have never been approved for sale, but technically individuals can import them.
The evidence for HTPs being healthier than cigarettes is thin.
I believe that overregulation of nicotine vapes is a form of protectionism for Japan Tobacco, which the Government of Japan owns a large stake in. This is a clear conflict of interest.