Well, the Yoko theory is something that at least won't mess up the entire story plot!
The Megure theory will be too big of a change with his background (him meeting his wife, etc.).
Also, all the intros and movies and fan art in the past that showed him as a friendly guy will be void.
Yoko never appeared in an intro or movie, and she is almost never portrayed in fan art.
My theory is:
Vermouth is her favorite as a "best friend" of some sort. I don't think the Boss and Vermouth's relationship is anything more than that. As for her being friends with Hidemi, I think this is because she starts getting suspicious that Conan might be Shinichi and that Gin failed in his attempt to silence the pesky detective. Ever since the first real episode (the one where Yoko is first introduced with the suicide) Yoko might have been suspicious that Kogoro is not the man he really seems to be. As the story plot advances, she gets so suspicious that Yoko finally tells Kir to investigate. Kir is having minor problems with the doorbell ringer, but it's good enough to ask Kogoro help for. So Yoko and Kir make an excuse and ask Kogoro to solve the simple case, when their main goal is to see whether or not Conan is behind it all. Eventually, the case is solved and Kir phones Gin and tells him she had a small problem and nothing is the matter any more. She was probably told by Yoko to investigate but not tell Gin anything about it. Whether or not Yoko is certain Conan is really Shinichi, I don't think she'd want to kill or get rid of Gin possibly because she doesn't want to lose such an important member.
That's just my theory, and it's not much, but it's something.