Cruise flight indicates that total lift and weight of aircraft cancel and thrust forces generated cancels with total drag forces. However, I am looking closely at the nacelle instead of the whole aircraft. Would the strut that connects the nacelle to the wing still experience reaction forces during cruise flight? Since engine thrust generated is greater than engine drag and lift on the engine is larger than weight of engine it sounds like even during cruise there needs to be a reaction at the strut to fix the engine to the wing, unless I am misunderstanding something.
Yes. The structure that joins the engine mount to the wing, nacelle, pylon, or whatever, has to transfer all of the forces being produced by the engine and propeller or fan, and their mass, to the wing box, and these forces are certainly present in cruise flight.
So you have the thrust of the propeller/fan applying a tension load forward pulling the airplane along, the torque reaction from the prop applying a rotation load trying to twist the nacelle, the weight of the engine and prop trying to bend the nacelle downward from gravity and G loads (where are there all the time unless the plane pitches over into zero G flight), and gyro precession loads from the propeller/fan trying to bend the nacelle to the side or up and down when the airplane yaws and pitches, and they would all be present to one degree or another during cruise flight.
You could eliminate the thrust and torque reaction loads by reducing power to remove those forces, but you can't do much to remove propeller/fan precession loads or gravity related loads while in flight.