So much research has left me confused! To book or not book trains?

My wife and I are going to Japan from September 10th to September 30th. It's our first time so we're doing Tokyo –> Kyoto –> Osaka, with day trips to Fuji, Hakone, Nara, Hiroshima. As well as maybe kanazawa, Nagoya and Kobe.
We keep seeing mixed reviews on whether or not to prebook our shinkansen and if we do, where to even book it from!
We've only traveled to Europe and usually book a ticket from one city to the next a few days before, while in that country and only pre book flights. A lot of people have said to prebook train tickets in Japan rather than do this. What are your experiences and if we need to pre book, where from!? JR pass? Klook? Rail Ninja?

Thanks in advance!