This is always a possibility, but not likely, the aircraft have always had pylon mounts, pylons and missiles fitted, in the mid seventies it was decided that there was no need to carry missiles on these pylons and we removed them. The aircraft would have gone through flight trials and wing load testing, so it could be assumed that to re-use them would not be a problem. I understand what you are saying about Afghanistan, in that a lot of factors could come into play that might not of been considered, least of all the weight difference between the BOZ pod and it's pylon compared with the weight of the missiles on their pylon that might give rise to higher wing flutter, thus fatigue cracking. The turbulance plus heat should not be much difference to the flight profiles that used to be flown (from memory) out in Malta/Cyprus and a few other hot places. Not knowing the flight profiles flown by the current deployed Nimrod aircraft or their equipment fits, I can only say that this is my thoughts on the subject and again I stand to be corrected by those that are more current/have better memory/knowledge than I have shown.
regards Exrigger