Why is 12V the standard for LED strips?
12V might be the "quasi" standard because of the 12V car batteries/electrics that were there years before the LED strips. 

Of course no one is driving a single 3V led with 12V and a resistor directly. That would be too much energy loss. 

Since there exist DC/DC converters which can transform voltage with a good efficiency from one voltage to another, it does not matter so much what voltage is used as primary source. 

Another thing is that you can put the LEDs in series until you get the required voltage (4x 3V = 12V).