The pilots are normally facing the same direction as the guys breaking through the doorway. Therefore, they not only need to turn around, they have to get thier weapon ready. I assume the pilot's wouldn't have their gun in hand at all times. If someone comes crashing through the "fatal tunnel" of a cockpit they have a disctinct advantage. It would be like shooting fish in a barrel.
STC: With the armored doors, it will take some time for the hijackers to break down the door. A minimum of 30 seconds I'd guess. Anyone with a modicum of training can draw a gun from a holster, turn and hit that target within 2-3 seconds. I base this estimate on my training (at SigArms Academy, Smith & Wesson Academy, and others) and also based on timing at competition. If the guns are kept in a lockbox with a pushbutton combination, maybe add a couple seconds to that.
Either way, by the time the hijackers break through the door, the armed pilot will already have his gun in his hand and be facing the door. When the door bursts open, the pilot will be ready to fire.
Try this: put your cellphone a holster on belt. How long does it take you to remove the cellphone from its holster and twist around in your chair to face behind you? A second or two at most?
Some day, in the near future, there will be an incident where a shot is fired in the airplane or a gun will go missing.
From the early 70s to mid 80s, many US airline pilots routinely carried handguns in the cockpit. The doom and gloom that you predict never happened.