Interesting thought...
Does Kevlar (in a Flak Jacket) show-up on X-Ray machines???
If not, then a determined terrorist has an obvious way to get onto the flight-deck, and get his hands on a weapon.
OK Lets say it does.
Then a member of the aircrew would make a pretty good shield.
For me its clear.
Keep the guns out of the cockpit. Whilst they are known to be there, they just become one of the 'considerations' for the would be terrorists. Do any of us think these extremists might be afraid of an armed and semi-trained adversary. Not for one second.
If you need guns on the flight, keep them with the Marshalls. If you need 10,000 Marshalls in the USA (not my figure, its in a prior post), then thats the cost of flying more safely which the Airlines (and therfore the passengers) might have to pay.