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I'd say for launch and recovery structure (nose & main gear, hook and keel) they are pretty close, but the strike missions tend to have higher launch and recovery weights so the strike missions are a little worse. The cat tow loads are bigger and so are the impact landing and hook loads. Maybe you can compensate for this by speeding up the ship a few knots (wear out the ship in place of the jet). For the up and away part, the strike missions are much worse for the wings, wing support structure and stabs, because they tend to do a lot of yanking and banking at high weights, low altitude and high speed. The CAP mission is a lot of smooth racetrack patterns so it's easier on things. If you want them to last, don't practice strike missions, or at least keep the gross weights down somehow, and don't operate them from ships.
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Ground loads are significant contributors to fatigue damage. On the ground, fuel in wing tanks and wing stores stress the wing like negative g. Get the wings flexing while you are taxying and the wing feels big negative g. Loaded aircraft miss out on most of this during carrier ops. Obviously, all wings experience negative g stress when landing, due to their inertia. Landing with a lot of fuel in wing tanks and all your wing stores does a lot of fatigue damage. This can be minimised by landing with fuel in the fuselage tanks only, or in the inboard wing tanks only if you can't get all the fuel into the fuselage.
Fuel in wing tanks, and wing stores, actually reduce the fatigue damage done to the wings, as they relieve (counteract) the lift loads on the wings and reduce the shear force and bending moment at the wing roots (the most highly stressed part of the aircraft structure).
Of course, having a light aircraft and not pulling g reduces fatigue damage also.
To illustrate: your aircraft weighs 50,000lb; you have 15,000lb of fuel, 10,000lb of fuel and the structure of each wing weighs 1,000lb.
Ignoring any lift effect from the fuselage, each wing has to provide 25,000lb of lift in straight and level flight.
If all the fuel and stores are carried in and under the fuselage, the shear force at each wing root, in straight and level flight, is 25,000lb minus the 1,000lb weight of the wing structure itself ie 24,000lb.
If all the fuel and stores are carried by the wings, the shear force at each wing root, in straight and level flight, is 25,000 minus (1,000 + 15,000/2 + 10,000/2) = 11,500lb.
Pull 6 g: the wing root shear load is 144,000lb for the first aircraft and 69,000lb for the second.