>> since all trains, including the Shinkansen, have at least some, if not all, non-reserved seats.
Many "scenic" trains, and some Shinkansen are 100% reserved seat only.
One morning I arrived at Tokyo Station from the Sunrise Seto night train. Checked to see what Shinkansen I can get on to spend the half day. Well quite a few of those going north are 全車指定席 100% reserved seat only.
For hotels I use Jalan and Rakuten apps. Sometimes I book just 30 minutes before arrival.