They said
Yoda : There are always two no more no less, a master and a appretice
mace:but which was killed the master or the appretice?
they did not know which was killed! hence mace's last line..
and thats because the darkside of the force clouds their view, they might have figured that the aprentice was not strong enough yet to take on two Jedi...so the master came.. but it is mainly because of the clouded vision and like it was said the sith have been gone for 1000 yrs.. how could they have known?
A few things. First, after encountering Dooku, you would think the Jedi's would assume that Maul was the Sith Lord, and Dooku was his apprentice. They have only seen two siths at that point, and the timeline doesn't match up that Dooku is the Lord and Maul is the apprentice. They must have suspected that Maul was the Sith Lord, and that he convinced Dooku to leave the jedi order and become his apprentice. Only when they found out that Palpatine was the Lord could they know the missing peice. Before that, it's all assumption. But I think it's safe to assume that Maul is the lord, and dooku is apprentice from their point of view.
Secondly though, Maul is dead when Dooku tells obi wan that the senate is under the control of a sith lord. So if Obi thinks he is telling the truth, he has the answer. Neither maul or dooku are the lord. If he thinks he is lying, he just has to assume that Dooku and Maul were the only two I guess.
Lastly, Qui gon was respected as a very powerful jedi. For a sith to take on Qui gon and obi wan at the same time, the jedi's very well could have assumed that it must have been the Lord to do that.
This is pretty simple... The Jedi did not make any assumptions. They prefered to keep both options open.
As for Dooku, there is the fact that he told Obi-Wan the senate was being controlled by a dark lord of the sith (And Dooku clearly does not control the senate) and that Dooku was a Jedi master, revered and respected until his disappearance after TPM. For him to have lead a double-life and been the top Sith lord was pretty unreasonable considering Yoda himself was Dooku's master. The idea behind the Jedi's thinking was that a Sith could not exist without being found out by the Jedi... not in their midsts. Of course, they were wrong. Shows you how accurate their intuition was at this time.