Early Comets suffered structural failures at cruise altitude due to the (then) poorly understood behaviour of metals under cyclic loadings. The 737 and the Comet 4 (on which the Nimrod structure was based) were designed later when there was a better understanding.
But all of that is irrelevant, because the fatigue failures were associated with the pressurisation stresses of high-altitude cruise. The ruggedness assessment you refer to concerned manoeuvring stresses at a few hundred feet over a storm ocean. IIRC no Nimrod ever suffered a structural failure during these manoeuvres. This was (at the time of the RMPA ITT) cited as a cardinal mission requirement, and none of the modern airliners were deemed rugged enough to meet this requirement.
In the subsequent P8 procurement the RAF were simply told that there was no available aeroplane that could do this role, so they would need to accept that this mission was no longer possible; they would have to use the sensors from medium altitudes instead. That's why the P8 is now an acceptable platform where it wouldn't have been before. AIUI there is still a "spirited debate" over whether two engines are sufficiently safe even without the low-level mission. No doubt that will be addressed in its MAR recommendations.
PDR