I hadn't noticed this.
I do recall that the NEX started out as an entirely non-smoking train. And then a few years ago, I was surprised to see a smoking car introduced onto the NEX.

I inquired as to the reason - and the JR employee told me that the smoking car had been introduced in response to "customer complaints."
And what exactly was the nature of those complaints?
"Customers were complaining about people who were smoking on the decks between carriages and the smoke travelling into the carriage."

So - JR put in some smoking cars in the hope that the smokers would sit where they were allowed to smoke. But in my experience, many smokers still prefer to sit in a non-smoking car and have a smoke in the space by the door.

Perhaps the trains should be equipped with a smoking deck on the back of the train - an open area like on the back of the old buses in Paris. That would be pretty cool.