This wouldn't be the first time that shadow magic and Illithid tadpoles have been put together.
2e had a monster called a mozgriken, which was a Svirfneblin gnome infected with a tadpole, them put through a ritual involving shadow magic.
Svirfneblin are usually not good tadpole hosts, Gnomes in general aren't and can produce odd results, but using a different ceremorphosis processes, they can turn Gnomes into a useful creature. As already mentioned, Netheril was all about the shadow magic, and they had some of the best and most powerful magic users for their times, so if I needed some shadow magic rituals for some reason, that would probably be the place I'd go.
The ultimate question really remains, what is the ultimate purpose behind our modified tadpoles? We don't know. We're clearly similar to the true souls, but not quite the same.
I still like my Illithid sleeper agent theory, even if it has holes in it.
