How long has the Black organization known about Kudo?

[Anastiza]

Haibara states while Conan is watching the soccer game, "Kudo-kun I think you've never thought that you've been in a secret mission our organization started half a century ago. You were already heavily linked"................that's 50 YEARS! so what, do they somehow have connections with Kudou's grandfather because Yusaku is only about 40, so when and how did the organization become acquainted with the Kudo family. A theory of mine is what if Shinichi's grandfather is the boss?

[Chekhov MacGuffin]

Haibara states while Conan is watching the soccer game, "Kudo-kun I think you've never thought that you've been in a secret mission our organization started half a century ago. You were already heavily linked"................that's 50 YEARS! so what, do they somehow have connections with Kudou's grandfather because Yusaku is only about 40, so when and how did the organization become acquainted with the Kudo family. A theory of mine is what if Shinichi's grandfather is the boss?

The Black Organization doesn't necessarily know about Shinichi. That quote properly is "Kudo-kun? You would probably never even dream that you are already part of a project the Black Organization has been working on already for half a century."

 

Basically it could just mean the APTX 4869 project that Shinichi was "forced into" against his will when he was drugged by Gin is part of a research scheme that began over fifty years ago.