I think it's managable thing to do with the new logic system.
You have your "alarm" button somewhere in your ship like in the cockpit. You connect it to each light with a AND door between. link another button to this AND door to make a ON/OFF button for the light (at the condition your alarm button is "ON") but if you press your alarm button to set it OFF every light connected to the AND door will be set off. Connect some red lights to your alarm button with a NOT between and the red lights will light to indicate the alert.
If you can find a way to clock them (1sec ON - 1sec OFF) we could make them flash.
Sorry for my bad english