Although this scene is only present in the book, the Siths' preparations make very clear that Dooku knows the entire thing is a setup and speaks with Palpatine as he does with Sidious in the films.
Indeed he did. Dooku (aka Darth Tyrannus) knew his master's identity. At this point the Jedi thought Dooku was the Sith Master. The kidnapping was planned to reinforce public support for Palpatine while further confusing the Jedi about his true identity.
Atleast those knew for sure that palpatine was darth sidious before he became emperor of the galaxy. Count Dooku definetly knew, Mas Amedda, Tarkin, and Maul possibly knew.
In fact, he even planned on replacing Palpatine before Order 66. Out of all the Sith seen throughout Star Wars, Count Dooku still stands apart from them all. While he was undoubtedly evil, he often had a calm politeness rather than maniacal behavior.
While many viewers might describe Count Dooku as evil, he ultimately had a vision in mind for the galaxy, with the hope of bringing peace, justice, and security to his new Empire. He likely believed his version of the Empire would have been far less oppressive than what Emperor Palpatine eventually introduced.
What If Dooku told Obi Wan that PALPATINE is Darth Sidious?
Why didn't Count Dooku have Sith eyes?
While Dooku may be powerful enough to hide his Sith eyes, there is another reason for his unusual appearance. Dooku's eyes were never yellow because he did not have the same motivation and emotions as other Sith. Dooku was an idealist who left the Jedi because he thought they had lost their way.
Dooku and Yoda have had a long history. Master Yoda trained him, but Dooku also trained Qui-Gon Jinn, Obi-Wan's master. The lineage of master and apprentice runs deep, and it was Dooku's fall to the Dark Side that hit Yoda very hard.
Star Wars: The Clone Wars portrayed Dooku as Palpatine's willing co-conspirator, clearly well aware the clones could (and would) be turned against the Jedi. Although he tells the Kaminoans this is just a contingency, his comments to Darth Sidious confirm he expected Order 66 to be given.
A Sith Lord with the ability to cheat death and create life, Plagueis is the enigmatic mentor of Sheev Palpatine / Darth Sidious, who, in accordance to the Sith's Rule of Two, eventually betrays Plagueis by murdering him in his sleep, taking his place as Sith Master.
Even in the old Star Wars canon, the two had a confrontation, as they met in the comic book Star Wars Tales #9, where Maul pieced together that Anakin was Vader.
Sidious revealed to Maul that he did not intend to kill his former apprentice, as he still had use for Maul; it was Sidious' hope that Maul would lead the Sith to Mother Talzin, Maul's mother and the leader of the Nightsisters, so she could be eliminated as a potential threat to the eventual Sith rule of the galaxy.
Maul most likely knew Sidious' double role as Palpatine and Sidious when he served as Palpatine's apprentice. He definitely knew about Palpatine's goal of creating a galactic empire ruled by the Sith. Maul knows that Sidious is the Emperor.
Even though they were both trained by Palpatine, Dooku and his predecessor, Maul have been enemies every since his mind was restored by Mother Talzin. This is because the two hated each other.
The reason Dooku joined the Separatists, he said, was that he learned a terrible truth: a Sith Lord called Darth Sidious controlled the Senate. With Obi-Wan at his side, they could destroy the Sith.
When Dooku was still with the Jedi Order, he was considered to be one of the greatest (if not the greatest) lightsaber duelists of his generation. Anakin really wasn't as good of a duelist as many people hype him up to be.
However, joining the Sith means declaring loyalty to the dark side, which Anakin did before his eyes turned yellow. This may explain why Kylo Ren, torn between the light and dark, didn't have yellow eyes in the Star Wars sequel trilogy, as killing his father split his spirit even more.
The most agreed upon theory, started by Reddit user Lumparoo in 2016, is that Jar-Jar is a powerful Force-user conspiring with Darth Sidious. In addition to this, some believe he either trained, or was supposed to become Supreme Leader Snoke, or that he is a reincarnation of Darth Plagueis.
Sidious may have given Dooku the title of Darth Tyranus, but because the Jedi Order knew him as Count Dooku, greatly preferring to not indulge his role as a Sith, they continued to call him by that name.
