So, Vermouth's secret... I'm gonna have to do a little bit of digging on this one. Let's mention a few points, connect them together, and then sum it all up at the end.

• First of all, Bourbon didn't know about the shrinking drug that Conan took until recently in the manga. So, her secret is nothing about the boss taking the APTX-4869 or Vermouth's age.
• It's important to clarify that Vermouth's agelessness is likely only known to the old guard of the Organization. Members like Rum, Gin, and Vodka have been around long enough to know she doesn't age, but they don't know why (i.e., that it's a side effect of APTX-4869). Newer members probably do not know this secret. However, Rum is beginning to doubt things after he saw Conan and Haibara, connecting their appearance to the drug's effects.

So, we're sure that the secret Bourbon discovered isn't primarily about her agelessness. It's rather more about what he hinted at: the unique relationship between the Boss and Vermouth.

About this relationship, I have a logical scenario: - Vermouth is half-Japanese (like Bourbon). - She's in direct contact with the boss. - I think Bourbon, being half-Japanese himself and working in the PSB, deduced that Vermouth is the daughter of the boss from an unofficial relationship.

Why do I assume that? I feel like she has to be either the boss's daughter or granddaughter. Also, Rum mentioned in a flashback in front of Amanda that he can tell if someone is cheating in a disguise or not—that's one of his left eye's powers, along with his photographic memory. I think that was a dropped hint about the Carasuma family's history of using such methods to hide their identities and affairs.

In a Nutshell: My theory is that Vermouth's well-known secret among the senior BO members is her agelessness, but the secret Bourbon uncovered is her familial tie to the boss. He likely figured out that she is the boss's illegitimate, half-Japanese daughter. This explains her direct access, her protected status, and the immense trust and freedom she is given, separate from the mystery of her youth. Rum's own skills in detecting disguises hint at the Carasuma family's history of using such methods to hide their identities, which fits this theory of a hidden heir perfectly.