Did she just pull out her Snail and talked to Vegapunk while CP agents, including Lucci, wear standing next to her? Wouldn't they wonder why Stussy was offering help to someone? Wouldn't they see that she was talking to VP because the snail would have his features? Couldn't she and Vegapunk talked about it before CP0 arrived? Why would Vegapunk even have to tell Stussy that he is in a bad situation? She knows it because she is involved in causing it. She can see it.
Another optioin is that Stussy is not the mysterious ally. Lucci is not obeying orders. He is not waiting for Kizaru. He is destroying valuable inventions. So Stussy is trying to restrain him and Kaku, until the others arrive. She is seeing that they are losing and causing havoc. She is still on the WG's side, just prudent.
Another optioin is that Stussy is not the mysterious ally. Lucci is not obeying orders. He is not waiting for Kizaru. He is destroying valuable inventions. So Stussy is trying to restrain him and Kaku, until the others arrive. She is seeing that they are losing and causing havoc. She is still on the WG's side, just prudent.