I think it's because the train system is really developed over there and faster. So if the trains were to be unavailable, taking the bus would take a long long time
This is just my experience as a repeat tourist but I’ve barely used the bus when I traveled there cuz it’s much more convenient using the train.
You're right, if their train system is super developed the it would make sense to almost forget that buses even exist. And I reckon their bus services are most likely underperforming because of that so maybe they don't even run late at night.
I don't know about Japan, but I know in Korea, it's mostly a money-saving thing. If it's late and the trains aren't running, I could technically take a taxi if I'm that set on getting home, but that'll cost me a good bit more than just crashing with whoever I'm hanging out with until the trains are back up in the morning. If it's not too late, you could take some busses, but you'll need to figure out where to transfer and how many times, and sometimes you have to pay between transfers, so again, it's easier and cheaper to just go to someone's home if they offer.
Thinking back on it, it’s either the train or walking. Taxis are expensive in Japan. The only time we used a bus was at the airport when we have to move to another terminal or the Disneyland one lol...
Do people in Japan use the bus often? I know that the "train stopped running" trope is there to get the couple together but in real life people would try to get on a bus yet they never even seem to consider that option in mangas, sometimes they even walk home instead.