Yes there is still separate security for direct US flights and also alll El Al flights.. The schematic earlier in the thread is accurate as of July.

The check in desks for all such flights are at that end of the terminal and feed directly in to that "special" security. Although signage isn't so clear, apparently "priority" on your boarding pass let's you use the security priority waiting lane - was only one screener in use when we came through.

At 8:45am when AA check in deals opened, there were more folks in the priority lane than the main lane for check in.. Assume it is like Miami where if you are priority you can use whatever desk you want! They did adjust so there were 3 priority designated desks going.