Do you know how much of a big difference it is to allow your units to fight in full strength even when damaged (particularly if you have units like Archers and Siege Units)?
I do, in fact. It's, at best (when a unit is nearly dead), a 33% bonus. Except - because post G&K introduced the 100 hp mechanic - units don't die as easily now and you'll almost never have units almost dead and still in the fray. Usually, your units in the fray will be getting somewhere around a 10% bonus, which is nice, but not game making. Bushido is nice when it enacts a miracle and saves your scout from a swarm of Barbarians (post-G&K, I had a scout survive on 1HP solely because of Bushido) or when you're making that last push to take out a city, but in the end, the Bushido bonus rarely comes into much consideration.
And the Zero is still a lousy unit because Fighters are lousy in single player. Fighters are decent on defense or for baiting out ant-air, but you'll likely never use them on the Domination path because a swarm of Bombers is just more effective. The Zero comes late, with lackluster bonuses, costs as many hammers as a Bomber to build outright, and the lack of an oil requirement isn't really enough to encourage you to build them.
I say these things as a Japan fan. I almost never play anyone else. I'm grooving on the additional fish-culture, and I am well aware that the Samurai is an amazing city-sieging machine. (Though the latest patch, removing the quick upgrade of Samurai to Musketmen, has ironically increased Japan's reliance on finding large iron deposits.) Japan is an okay Civ, and the one I want to play, but it is not the best Civ for pure domination. Thankfully, it no longer is trying to be.
Yes, but Japan is much stronger now than in vanilla.
Not true, I'm afraid. In Vanilla, Bushido was regularly viable because your units were so often almost dead. Kamikaze style attacks were rewarded in Vanilla (and Japanese units would often walk away from such attacks very much alive in any event). But post-G&K 100hp change, that's no longer the case. It makes much more sense to remove wounded units from the battlefield and heal them now, so Bushido rarely takes effect.
Additionally, in Vanilla the penalty for heavily injured units was
50%; G&K reduced that penalty to a maximum of 33%. These two rules changes were a heavy nerf for Japan.
Finally, the Zero became even less viable post G&K with the introduction of the Great War units. It's so late in the tech tree, you'll almost never get to the point where you can use it...if you even wanted to.
Japan was at the height of its power in Vanilla, when it was considered one of the best Civs in the game. Then the game evolved and Japan didn't evolve with it. Japan was a domination monster in Vanilla, but it is now a solid average Civ.
Japan's UA isn't great because it mostly helps melee units which suck and because you shouldn't be losing ranged units at all. Japan gets two military UUs in very different eras that it can't conquer the world with (compare with Keshik+khan, longbowman, impi, siege towers, horse archers).
Have you ever faced down a swarm of Samurai? A proper Samurai swarm can take down an open-terrain city in one turn. My world conquering usually hits its heightened pitch the minute I get Samurai online.