Exactly, I doubt the plane could shield from gamma rays. Not only that, but if a nuke detonated closely enough the shockwave and heat would cause the plane to at least fall out of the sky. There’s only so much metal you can put into a plane before that plane becomes a brick. Then there’s the plane hitting the ground, which is going to hurt even if the frame holds together.
The POTUS is better off heading to a designated Fallout shelter.
The plane is EMP protected and has shielding but could not withstand a close encounter with a NUDET. The plans are written so that the aircraft will fly to a preplanned area where there probably will not be nearby nuclear blasts. If leaving from Andrews AFB near DC the easiest thing would be to get out over the ocean away from all the east coast targets (my guess). If it is located somewhere else while the President is visiting they have areas mapped out that are considered probable safe zones and that is where the aircraft will fly.