How the Soul Society figured out the "Masked Army" existed
Here's the thing that just hit me from the Hell Arc oneshot of Kubo's. The Soul Society knew 12 years after TBTP that Shinji and the others had to be alive.
Konso Reisai is done 12 years after a captain's death (Bleach ended 10 years after TYBW finished, so this is two years later). Kyouraku mentions that it's something shinigami learn at the academy, and as Renji says, it's not done terribly often, because captains don't die very often.
During TBTP's past arc, Love, Kensei, Rose, and Shinji are all captains infected via hollowfication, and therefore have a spirit class of 1, 2, or 3, based on what Kubo's stating here.
The soul society knows what hollowfication is, because Kubo stated in one of his Klub Outside answers (#548) that there was a loose organization of researchers prior to Kisuke founding the Research and Development department in Squad 12. (It's how Mayuri Kurotsuchi and Senjumaru Shutara from Squad Zero knew each other previously).
Kisuke recognizes what is being done to Hirako and the others as hollowfication immediately, which indicated the Soul Society is already familiar with what the process looks like and what happens to the victims. Since the konpaku prior to that were vanishing without a trace, there was no way to conclusively know that hollowfication and soul suicide was happening.
In other words, the Dai Reisho Kairo likely has tons of records stating conclusively that anybody that's hollowfied is going to have their konpaku break down, resulting in death. There's no known way to save them, all they can do is put them down like animals now.
Except of course, they vanish, along with Kisuke, Tessai, and Yoruichi. No matter. Those hollowfied shinigami are basically as good as dead, and since four of them were spirit class 3 or up, Head Captain Yamamoto is going to know damn well that there has to be Konso Reisai for them, because their reishi is too dense to reabsorb.
Kyouraku knows what a konso reisai is because he's learned it at academy and seen it more than once, but in the Hell Arc, things are behaving differently due to so many captains dying and throwing the balance of Hell off-kilter. Yamamoto also didn't exactly get to hand over the reins and tell him all the secret Head Captain things, so his ignorance of the latter part of that ceremony involving hell makes sense.
Shunsui has never had to do this before, doesn't have all the info from the previous Head Captain, and the ceremony doesn't usually look like this, is what we can infer from those panels.
So what happens when shinigami try to do a ceremony for a captain that's NOT DEAD AKSHULLY?
I think it would also be off in some subtle way. And since he's the only captain that likely knows what one of these ceremonies SHOULD look like, he may have kept quiet about it.
I think Yamamoto got everybody together to send off four captains in 1912 and internally went, "Oh, shit. They're not dead. They've gone renegade." And you can kinda see that concern later on. If Yamamoto's dealing with more than 3 defected captains, he knows he's about to have a bad day and needs to put them down fast.
I also think Kisuke and the others had a genuine "oh shit" moment when they realized they only had about 12 years before the Soul Society started actively looking for all 11 of them, not just Kisuke, Tessai, and Yoruichi.
Now, would Yamamoto admit that openly? Hell no, he's kept things secret before to avoid spreading panic. So by the time people start possibly hearing of these "masked army" folks within the rank and file, a lot of people (like Isshin and most of the captains by the time the story starts) wouldn't know specifically that the masked army was Shinji and the others.
After all... they GAVE them a konso reisai.
Can't be those guys... right?
(And you better believe not everyone took whatever bullshit cover story Central 46 spewed at face value afterwards, either. Our boy Shunsui sure as fuck didn't.)