The modulus of elasticity of aluminum does not change with cycling (or basically with anything else but big temperature differences).
Fatigue is a damage accumulation process, that does not show in the most obvious properties, like modulus or strength.
The aviation regulations changed a long time ago from requiring to avoid cracks to requiring to have structures that can operate with cracks long enough to for them to be detected, as is exactly the case here. Of course nobody design planes to crack, but the regulations reflect the realization that completely avoiding cracks is impossible ...