So far, my theory is this:
The Black Organization seeks the way to immortality. It must be one of their goals. That is why they have many biochemists and scientists of the like experimenting and researching in their facilities.
In one of the experiments made by some scientists, Vermouth was used as the test subject, and a drug or something was applied on her, causing her to either (1) Shrink ten years younger, like Conan and Ai; or (2) Become immortal, or stop aging. Both things might have happened to her. Maybe, after aging ten years younger, it was found out that she would not age anymore.
It is possible also that Shiho's parents are the scientists who possibly conducted this experiment, and maybe this is the reason why Vermouth does not like Shiho, and vice versa.
Then, because the experiment on Vermouth was a significant event in the Organization's attempt to seek immortality, the Organization decided to keep her as a valued asset and member, and also making her the Boss's favorite.
And maybe, since Vermouth is tired of what the Organization is doing, she tries to help Shinichi defeat the Organization, in order to set her free from the Organization's chains once and for all.
Well. That's what I've got. Just wanted to share.