In this paper, we give an overview of the issues one must consider when designing methods for vibration based health monitoring systems for perforated thin shells especially in relation to frequency response analysis. In particular, we allow either the material parameters or the structure or both to be random. The numerical experiments are computed using the standard high order finite element method with stochastic collocation for the cases with random material and Monte Carlo for those with damaged or random structures. The results display a wide range of responses over the experimental configurations. In perforated shell structures, the internal boundary layers can play an important role especially when damage is allowed within the penetration patterns. The computational methodology advocated here can be used to build statistical databases that are necessary for development of probabilistic damage identification methods.