I'm not sure why nothing would come up for that route. Perhaps you changed the search perimeters on Hyperdia by mistake? You can take the JR Nara line directly from Kyoto Station to Nara. It costs 710 JPY, or is free with a JR Pass.
Typically for the 'Route is not found' message, either the station names are not correctly input or you have changed the options to in/exclude JR or private lines under the options menu.
Comments
I'm not sure why nothing would come up for that route. Perhaps you changed the search perimeters on Hyperdia by mistake? You can take the JR Nara line directly from Kyoto Station to Nara. It costs 710 JPY, or is free with a JR Pass.
Best regards,
Japan Experience
As you can see on:
http://bit.ly/1TYIXuY
the route works fine. You can take either JR or Kintetsu, but needless to say, you can't use Kintetsu with a JR Pass.