My theory on EJ's plan..

 EJ told Sami that he's taking Johnny on a "pirate adventure" vacation (which is ludicrous for him with his daughter missing!).  I bet he's going to fake a plane crash/deaths so that he can start a new life somewhere with his children.  This answers the question of how he can keep Sydney away without abandoning Johnny.  Maybe he will make it look like the "kidnappers" killed Sydney, then announce that he and Johnny need the trip to get away.