"I think someone stated that an aircraft cruising at 45 knots into a 45 knot headwind would have zero kinetic energy, that is not correct. Kinetic energy relates to mass multiplied by speed squared and the speed for an aircraft in normal flight is the true airspeed, so any airspeed above Vs1 can still be swapped for gravitational potential energy even if the aircraft was moving backwards relative to the ground."
No. It is correct. Even tho Kinetic Energy is a scalar (V^2 = V*V is a dot product). Kinetic energy exists only where there's a relative speed between the objects in question. Thus the guy sailing at 45kts IAS into a 45 kt headwind has no kinetic energy relative to the earth.