A normal metal wing for instance can corrode and weaken with years of service due to water contamination, flight stresses, dissimilar metals used in construction ect.
I believe fatigue is a different issue than corrosion/dissimilar metals/water contamination. With respect to design, fatigue analysis doesn't typically deal with deterioration due to these factors.
With respect to composites, its extremely difficult to detect imperfections caused by fatigue. Delamination due to fatigue that are not indicated at the edge of the material are almost impossible to detect using commonly available methods.
Also, composite structures give little warning before failure. There is no "plastic" state as exibited with metal structures that have been fatigued. If you overstress metal, it may stick around long enough to get the airplane down, but composites tend to fail explosively. They don't fail "a little bit" like metal can...
Some work is being done in ultrasound technology, but I imagine it will be quite some time before you see this commonly used in the field.
Critical composite panels are currently manufactured with quite conservative safety factors until the maintenance industry catches up with the technology.