Hello,
I will check into this for you, and direct answer a few things that stood out to me.

>tried his passive damage
My understanding is that his updated skill is a mystery, not a passive. The Ultimate - Reverse Four Symbols Sealing. Is this the ability we are talking about, or something else?

> Did you really make his passive fixed damage?
I will look into this for you.

> Take Obito 10tails for example, his passive damge in even rounds is pretty good, why is Obito's passive damage superior to Danzo's passive?
TT Obito is a more expensive ninja. It makes sense that he would do more damage with his attack.
Looking at Danzo, the mystery is listed as "unavoidable damage" not massive unavoidable damage like, say, Hiruzen. It makes sense to me that his damage would be, well, regular.

>If his damage is fixed and it won't really change that you use him in a not-stacked position or in a stacked position, why bothering with an update?
Keep in mind that the game is designed to have balanced stats/equipments, not the stacking method most players here in the EN version use.
That said, the update was to give him the ability, not necessarily to make the ability so powerful he replaces most other ninjas.

OK, what I've been told is this.
As mentioned, his damage is just "damage" not "massive damage" or even increased damage or whatever prefix that ninjas like Hiruzen have. The damage is not supposed to be that high. It's comparable at best to a regular mystery. There are also some strange special addendums to it.
It hits the entire field, all six teams, making it fairly unique and capable of pushing a lot of damage. From what we can tell, the purpose is not to alpha strike a ninja like Hiruzen, but to finish off wounded ninjas after using the regular mystery or hitting them with other attacks. Additionally, he has a strange caveat that his damage seems to reduce the more targets he affects, likely for balance, which could lower the total numbers you are seeing.

It's worth noting that Danzo is not a top-tier ninja, nor has he ever been. Even in expensive shops, he doesn't seem to clear 10k coupons from what I've seen while checking, so when you say "no one will use him," to an extent you are correct, for your situation. No older players with established accounts will likely use him, except for niche situations, such as needing a deletion kill and not having Hiruzen or wanting some of his passives. However, I do know that a lot of newer players on new servers use him, so I don't believe it's accurate to say that "no one uses him" or that he's completely worthless. He's just a niche that is already filled for you.

As for the stacking thing, this may be a legitimate bug. If you can send me a video showing him in p1 gear and using the mystery and then p4 gear and using the mystery, I can submit a bug report for you. Obviously this needs to be real pvp and not arena.