The only one who clearly suspected they were up to something was Elaida, and she was paranoid enough to do so. She also came to that conclusion only after she found out Siuan was involved with Rand too.

Verin was certainly clued in, but she kept quiet about it. Cadsuane kept an eye on Moiraine and Siuan independently, but nothing she said indicates she knew they were working together.

I think most Aes Sedai thought Siuan and Moiraine's friendship had gone the way Siuan and Sheriam's had. Allies, yes, but no longer close friends.