Aside from General Griveous, in whom Tyranus trained, did the Separatist Leaders, specifically Viceroy Nute Gunray, Rune Haako, Poggle the Lesser, Wat Tambor, San Hill, Passel Argente, Shu Mai, Senator Po Nudo, and Senator Tikkes, know that Dooku was a Sith?
They probably put two and two together. People killed on Mustafar by Vader were in contact with Lord Sidious since Episode 1. He explicitly mentioned Sith to them when he introduced Dath Maul as his apprentice ("Not for a Sith"). They were not total imbeciles, so they probably spent some time researching history and figuring what Sith were (1000 years is not that long even on Earth, we have lots of books about Romans for example) . Also, Sidious constantly mentions his apprentices (" I am sending you my new apprentice, Darth Vader. He will... take care of you.") . If Darth Vader was new apprentice, they must have known that old one existed. Was Dooku introduced as apprentice is unclear, but they knew he had Force powers (ex-Jedi master), and he also obeyed Sidious, therefore conclusion is clear from that. One thing that they probably didn't know is Dooku's Sith name (Darth Tyranus).