The average Tokaido line Shinkansen is 16 cars long, with aroughly 1323 actual seats.

3 Green cars
(1 smoking green car, 2 non smoking)

13 Ordinary Cars
(5 Unreserved, 8 Reserved)
Out of the 5 unreserved 2 are smoking, out of the 8 reserved 2 are smoking)

In total there are 11 non smoking cars, 5 smoking cars or roughly :
963 non smoking seats
360 smoking seats

I don't have the data that shows how many passengers are actual smokers that travel in smoking cars and who were there because they needed a reserved seat, but the number of smokers in Japan is pretty high.

I'm not sure if I would go out and blame JR for the problem, I think they should make 1 or all unreserved cars non smoking to free up more clean space.

JR East has recently made the Narita Express all non smoking, so there seems to be some movement.
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Do you…
a) Stand for 3-4 hours

Nagoya is 48minutes West of Kyoto, a lot of passengers will depart either Kyoto or Shin-Osaka (15minutes later) there's a high chance you will gets seats if you are going beyond Kyoto/Osaka.

If not then its 2hrs East to Tokyo terminal if taking the shinkansen, I think that might be where one will have some problems.

But I understand what you're trying to say, it does create a problem.

Effective December 10

The Nagano Shinkansen will become entirely non-smoking + several limited express trains that includes the NEX.

Ashtrays will be removed from the vestibule areas of all JR East
shinkansen and express trains and these areas will be made
no-smoking.

The lounge cars and communal areas of the Hokutosei and
Cassiopeia sleeper trains will also be made non-smoking.