Japan was the one of the last countries to introduce non-smoking flights and smoking is still possible on certain trains, especially on Shinkansen.
It is not divided into smoking and non-smoking cars but there are smoking rooms which you can smoke inside. The room itself is very tiny; roughly 1.5 square meters, no seats, strong air purifiers and ash trays. It is not a place to talk with your friends but may be you can have an opportunity to chat with local Japanese.
Then, it is not located at all cars, usually the smoking rooms are located in each 3-4 cars, at the deck where lavatories are located. These smoking rooms are well announced on board and also mentioned usually on the table in front of you.
By the way, asking for lighter is not normal as in Europe and begging for cigarettes is much abnormal than in Europe. Please note that neither cigarettes nor lighter are sold on board. Please buy at the kiosk before riding the Shinkansen.