Ok. I believe its entirely plausible for Rukia to have never met Isshin. Seireitei is a very large military complex with a shit ton of people in it. However, I do not believe it is plausible for her to have not known that a man named Isshin Shiba was the captain of the 10th division 20 years ago. I am 100% sure that, though they may not have met them, all of the members of the Gotei 13 at the very least know WHO their Captains are. So, just spitballing off of the idea that Rukia at least knew his name. She gets her first real world assignment. Meets a boy named Ichigo who looks painfully similar to her dead, very close friend Kaien Shiba, who also just so happens to have a father named Isshin. Sure, its been 20 years, but Shinigami live a very very long time. 20 years really isn't that long of a time to them. Therefore, I can't believe that she never thought for even a second, "Hmmmm. Didn't we have a Captain named Isshin Shiba who mysteriously disappeared 20 years ago? Wait, how old is Ichigo?" I mean, seriously. That's not the only inconsistency though.
Any Lieutenant level or above shinigami who was so 20 years ago had to have known the extent of his abilities. Maybe nothing else, but if they knew anything about his powers, they had to at least know that his Zanpakutou was named Engetsu. Now. 20 years later this kid who looks suspiciously like a Shiba shows up in Seireitei with a Zanpakutou named Zangetsu. Sure. Isshin's Zanpakutou abilities appear to have been fire based. However, Engetsu and Zangetsu also share more than one abilities that are unique to their two Zanpakutou. I seriously doubt that Byakuya or any of the other Captains, especially Yamamoto, have never heard of Getsuga Tenshouu before. So I imagine that they at least would've been suspicous upon learning of Zangetsu and definitely smart enough to realize who he was when they saw/heard about Getsuga Tenshouu. Every single one of them cannot have just decided that was a massive coincidence. Especially Matsumoto and Hitsugaya. They were his lieutenant and third seat for god's sake! They had to have known of Getsuga Tenshou even if they'd never personally seen the ability used. I can believe that none of them ever met Isshin and would've never had the chance to personally recognize him. I cannot believe that they would be unable to put two and two together though. Maybe they simply kept quiet about it. They had to have known though.
These are the reasons that I believe Kubo Tite really just didn't plan out that reveal very well and simply decided it would be an interesting plot twist while he was writing that part of the story. I don't think that's too far-fetched. Especially considering the way things seemed to go completely off the rails about halfway through the Vandenreich arc. He just kept biggerfishing with the most powerful characters in the Bleach universe. Hyosube basically wrote Juhabach's powers out of existence and then Juhabach was like, "Wait, no. I'm god".
If he was just some random shinigami, all of these inconsistencies could be easily explained away, but he was a Captain!
Maybe he was only a Captain for a short time?
Even if he was only a Captain for a short time like a couple years, I feel like a Captain change is the kind of thing that the Gotei 13 would announce. Or if, not that word of it would at least spread quickly. I mean, it seemed like everyone in Seireitei certainly knew about Rukia's execution. I would assume that a new Captain appointment would be news that would spread in a similar way.