I was always disappointed in the reconstructed castles because they seemed to be built to suit a particular 1970s or 1980s idea of destination travel in Japan. Some focal point where a group would meet, take a group photo, and then go to some ryokan for a meal and karaoke and maybe another photo. The history and the authenticity of the "castles" were sort of secondary to the concept of the group (school, company, factory, club) travel. They weren't necessarily built to resemble the original. They didn't use authentic floor plans or architecture methods. They were steel and concrete with elevators and fluorescent exit signs and gift shops at the exit selling items that could have been made or sold anywhere, i.e. a keychain with Hello Kitty wearing a
samurai helmet - that kind of thing.
So visiting Nijo Castle for the first time was a nearly religious experience for me. It was the first castle I visited that had been kept in its original state. Authentic, largely untouched, beautiful, some parts in need of repair, but you could imagine that it looked mostly as it looked for the past 400 years or so.
But I think the times have changed and Japanese people are also seeking authenticity in a way they weren't in the 1970s. When I visited Shuri Castle before it burned down, I was really impressed with it, and I thought it a very worthy reconstruction. So I'm glad they decided to rebuild it. In this case, we know its a reconstruction, and it hasn't really existed in any useable form for a long while I believe. I think even before the war it was already mostly in ruins. So Theseus's ship doesn't come to mind when I think of Shuri Castle, but I know what you mean. I get more of a Theseus vibe from
Kinkaku-ji. I don't know why. Maybe it has something to do with being only able to see it from afar. So you can only gaze at a reconstruction of something that burnt down in the 1950s. And then had its gold leaf replaced/repaired more recently. You can't go inside, walk through its rooms, touch its beams, or sit in a corner and contemplate it. Its just a thing to look at and take pictures of. (But I still recommend seeing it, particularly if you can do it in the off-season months).
Ise Jingu... well this is the living embodiment of the paradox of Theseus's Ship. At least for us foreigners. I guess for Japanese the dismantling and rebuilding is the entire point of the structure, whereas us foreigners want to tread on the exact flag stones used centuries ago.