Actually, the astral duel worked in Sidious's favor. He may not have managed to defeat Yoda there, but the illusion was carefully crafted to ease some of Yoda's doubts. In the illusion, the clone troopers open fire on the Sith without hesitation and Dooku kills them. That helps reinforce Yoda's belief that the clones are good soldiers and can be trusted to the end. Also, Anakin fights Sidious without hesitation, raising Yoda's faith in Anakin, making it less likely that he would suspect Anakin of going to the Dark Side. And no, Anakin beheading Dooku doesn't count, as Yoda told him specifically that the Sith were to be executed.