Therefore, Yoda would have thought it was something else that was clouding the future... except he didn't. It was a crucial detail that was set in the place of Chancellor Palpatine, which we (spoiler alert) learn that is Darth Sidious.
In the same scene, we also see Yoda looking suspiciously over to Palpatine after he guessed what Amidala was going to say, and he was suggesting her placed under the care of a Jedi. 
Also at the end of episode 1, Mace Windu and Yoda discuss who Obi-wan killed: the master or the apprentice. They seemed to guess that it was the apprentice, and the panning shot out to Palpatine seems to imply that they were suspecting Palpatine, although it is not sure.
It is also noteworthy that in episodewas very soon after shown to be following the Dark Side, but it was also known by other associates of the separatists - including those who were captured and tried after the Battle of Naboo - so there was verification.
By Episode III, the Jedi knew that Dooku was the Sith Lord Darth Tyranus - we saw this confirmed in the Clone Wars series - and were using the name Sidious for their unknown second Sith opponent. They still did not know who Sidious was, however. The Epsiode III novelisation gives us this sequence:

"We have circumstantial evidence that traces Sidious to Palpatine's inner circle."
Suddenly Obi-Wan had difficulty breathing. "Are you certain?"
Mace shook his head. "Nothing is certain. But this raid - the capture of Palpatine had a be an