Shin is an odd outlier that I'm not sure how to factor into canon, or if Shin truly fits into canon at all. Shin existing with so many Mangekyou doesn't make all that much sense. I don't dislike the Shin arc, in fact I personally enjoy it, but I also think that several plot points and elements were contrived in Naruto Gaiden, so I'm just going to be blunt and say that I don't think Shin fits well into the Naruto-verse, although he doesn't necessarily have to contradict Sharingan lore, but simply adds to the rules of cloning in the Naruto-verse rather than adding to Sharingan lore rules.
Despite audaciously claiming the surname Uchiha, Shin is not actually an Uchiha, yet he has the Mangekyou Sharingan. And not just the usual pair of Mangekyou: his whole body is covered with the Mangekyou Sharingan, with the same patterning in each eye. So it appears that Orochimaru must've developed the technology to replicate and clone the Sharingan in addition to cloning people.
Shin's body had special properties, and somehow these properties recreated the same exact dojutsu over and over again. I'm not exactly sure how Shin's clones work, since the Mangekyou Sharingan would have been a dojutsu grafted onto him, not one he naturally possessed, so it seems odd that his clones would inherit the Mangekyou Sharingan genetically. Though maybe the Shin clones had the Sharingan transplanted into them at a later stage of their development, as Shin obviously possesses the ability to duplicate limbs and body parts, since his body had unique properties. That's why Shin was able to provide Danzo with the Sharingan arm.
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That opens up the possibility that Danzo's arm of Sharingan is not a collection of Sharingan stolen from multiple Uchiha, but rather one single Sharingan and clones of that same Sharingan. After all, Danzo did say that the way he had gotten his arm full of Sharingan was a "long story", and he neither confirmed nor denied that the Sharingan had been stolen from the Uchiha murdered on the night of the massacre.
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For all we know, Danzo could have had the arm before the Uchiha massacre ever took place. I imagine warriors go missing all the time so it would be entirely possible for someone who has as many resources and men under his command as Danzo does to trap an Uchiha, steal their eyes, and kill them and then declare them "missing", or frame an enemy for the Uchiha's death, or whatever. There were a lot of Uchiha before the massacre, so stealing a Sharingan from one probably wouldn't be too difficult for someone with a lot of influence, authority, and resources. Not saying that this is how Danzo got his Sharingan arm, but it's at least a possibility.
As for how Orochimaru acquired the Mangekyou Sharingan, that doesn't seem like it's out of the question either, since it takes an Uchiha witnessing the death of their closest friend to awaken it. Orochimaru has been around for a while, so there are ways he could have found and stolen an Uchiha's Mangekyou, or maybe he discovered an older one still preserved and hidden somewhere. The possibilities for how Shin and Orochimaru acquired the Mangekyou Sharingan are endless. Or perhaps Shin acquired the Mangekyou himself somehow.
While it's a weird scenario, I think it can fit with Sharingan lore (if not particularly well), but it adds to the rules of how cloning works in the Naruto-verse as well as the unique and unusual regenerative properties of Shin's body, which apparently can clone or replicate body parts, rather than contributing to the rules of Sharingan lore.
