how to not show two version app when open file in mac osx?
If you don't want the older applications on your backup drive to appear in the Open With menu you could drop the Applications folder of the backup drive in the "Prevent Spotlight from searching these locations" box within the Spotlight Privacy tab within System Preferences.

When Spotlight removes them from the index they should be removed from LaunchServices services as well. If after an short while they haven't disappeared then you might need to give LaunchServices a little nudge with the command from Chris Magnussen's answer.