Izanagi With EMS

[Shisui Namikaze]

Then Why nagato didnt use it...and madara and tobi are not using it.....

Because you have to have senju and Uchiha DNA. Nagato didn't have either one.

 

[-Vegeta-]

Even with ems if the user uses izanagi then the eye closes forever

 

[Shisui Namikaze]

The same rules doesn't apply for the sage. He used Izanigi. And he didn't go blind. It obviously does not affect him.