But these hints strike me as quite similar to the Jodie=Vermouth and Subaru=Bourbon "hints."
The one in contact with Masumi knows about what happened on that beach. Shuichi and/or Shukichi could've heard about it from Masumi. Also, both Shuichi and Shukichi met Shinichi/Conan before the Bowling Alley Murder, and both know he is a brilliant detective.
If Shuichi/Subaru is in contact with Masumi, she would tell everyone she's in contact with her other brother—Shuichi's supposed to be dead, after all. Since he's undercover, he wouldn't tell her what he's up to—he wouldn't tell her he's Subaru Okiya—she wouldn't know he's working with Shinichi/Conan, and, thus, would wonder how he knows Shinichi/Conan.
As for clues of this twist, the sleeve of the middle brother (File 860) was redrawn for Volume 81—it looks more like Shuichi's/Subaru's shirt sleeve from Silent Clash (700–704/578–581) than the sleeve of Shukichi's shogi outfit.
File 860 (Volume 81)
File 702
File 899
The key, here, is the color—Shukichi's sleeve is too dark, while Shuichi's/Subaru's is more in line with the color of the middle brother's sleeve.
Actually, Shukichi could've been there, at the beach, and recognized Shinichi's/Conan's face as Shinichi's—my point is that the one who contacted Masumi is bringing this up, over the phone, because it seems to me that Shuichi/Subaru is the one contacting Masumi.