Rep Power: 0

2012 Civic Si all stock. key fob unlocks all doors and running lights flash. However lock function only locks doors. No beep on 2nd press, no lights flash. All other fob functions work. Horn works. Hood latch seems to have an electrical connector on it but there's no wire to it. Does the 2012 Civic Si offer the beep / flash lights on locking? Could it be that the hood latch has something to do with it? My Haynes manual wiring diagrams do not show any connections that are helpful.

 
Rep Power: 245

Yes it could be the hood switch making the system not fully ready. Look for any wires near the hood latch they might have been tucked away somewhere.

It also might be a setting you can change. The feature is called lock confirmation.