During my stay in Kyoto for university, we had one vegan girl with us. We all thought she would suffer a lot due to everything having fish in it (dashi).
However, she managed really well. She found so many vegan restaurants and dishes that even our teachers were quite surprised. She also knew the most food-related Kanji of us all and thus knew exactly what to look for in stores/restaurants.
So yes, you can totally get by in Japan as a Vegetarian/Vegan, but you have to do a lot of research/looking up beforehand
Kyoto is a uniquely good place for vegetarian food in Japan - there are a lot of Buddhist temples from which the monks etc. follow vegetarian diets, and the traditional Kyoto cuisine is simple vegetable-based meals. Even someone who did the same amount of research might struggle in Hakata or Sapporo.
Yes, Japan is actually not terrible for vegetarians/vegans, especially these days where even Mos Burger has good plant-based options. But you need good language skills and local knowledge. Even most Japanese locals won't know how to help.
For onigiri, there are vegan varieties even at combini like kombu, daikon, or ume-shiso. They don't have a lot of protein though. At a dedicated onigiri place you can often find natto, bean, tofu, or egg onigiri, as well as inari.
A lot of vegan restaurants are just marked as "Japanese restaurant" on Google maps. Many of them don't market or present themselves as vegan. There are especially a lot in Kyoto, which has traditional specialties like yuba and shojin-ryori.
If for any reason you want protein bars, Japan has a decent amount of them in drugstores (although I think North America's are better).
However, she managed really well. She found so many vegan restaurants and dishes that even our teachers were quite surprised. She also knew the most food-related Kanji of us all and thus knew exactly what to look for in stores/restaurants.
So yes, you can totally get by in Japan as a Vegetarian/Vegan, but you have to do a lot of research/looking up beforehand