Even in the US, every major city has overnight bus services. I live in Seattle and have taken the half hourly to hourly bus home at 3am before. It's wild to me that Tokyo has none.
I will say that there are businesses that has stepped out to fill this void: there are numerable “Internet/manga cafes”, that have private rooms where you have reclining chairs where you can nap; you can just rent a karaoke room for a couple of hours, some onsens have overnight options (including the same reclining chairs etc) - if you just want to have a semi-private space to nap, there are plenty of options.
Just coming home is difficult.