I seriously doubt the problem is lack of defensive measures.
IMHO, it’s more likely that someone dropped the ball and allowed the plane to be serviced by Turkish technicians, and they just didn’t know the condition of the airplane, and out of an abundance of caution, they advised the President to use another airplane with a known service history.
It’s like losing track of a piece of evidence in a criminal case.
"Typically, presidential transport aircraft are decked out with a suite of electronic warfare and defensive equipment, with the plane’s electronics hardened to withstand a nuclear electromagnetic pulse. The shortened modification timeline for the Qatari gift plane required L3Harris personnel to scale back the typical upgrade package."
They probably should not have taken the plane to Turkey at all until the upgrades are finished, but Trump may have insisted.