She called out to Calvados to stop firing because he was shooting at Ran (Angel), and Vermouth has a sentimental attachment to both Shinichi and Ran because they saved her in New York when she was disguised as a serial killer to lure out Akai Shuichi.
The "Silver Bullet" is a reference to a person who can destroy the organization, but it's unclear if we can link it to the drug (or if it's even the same one as APTX4869, probably the same project though)
I'm not talking about Atsushi Miyano's appearance in the anime, I'm talking about the manga (although he was mentioned by name in the manga, obviously). I believe when Gosho said that the boss had appeared, it was partial to the manga, and it was quite some time ago as well, towards the beginning of the series. After all, Detective Conan wasn't expected to last that long, let alone 20+ years.
"Maybe" is the key word there. It could be awhile until we know for certain why it is that she doesn't age. Where does it say that APTX has a 1% chance as well, as far as I know, shrinking was just a rare side effect...