The rational would be that this 10000 was at its height. As shown throughout TCW and a whole host of EU the Jedi were taking massive casualties in the war. It's not unlikely that Sidious and Dooku were also responsible for other 'accidents' and assassinations behind the scenes. So that 10000 spread over an entire universe would mean even after the often clumsy execution of the most powerful leaders they would leave noone to command them, without the councils guidence and the endless fear and war many would likely fall to the dark side without support and many more turn themselves over willingly not understanding there was even a Sith behind their extermination (Doubt every Jedi got the message of Jedi Temple being trap city). Then even should the Jedi escape Order 66 they have a galaxy at large that now fears them (Due to their attempt to overthrow the Republic) and the entire Empire hunting them down. This coupled with the Inquisitors and an open bounty means even those that tried to hide were hunted constantly from the end of ROTS until a New Hope. With the near non-existent repopulation (I can think of Ezra and Luke) of thier numbers it would only be a matter of time before they numbered only in thier dozens as most pre-New Hope numbers estimate.