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We expose an efficient strategy to deal with shape optimization of dynamical systems exhibiting flutter-type instability induced by friction, such as the considered disc-pad system. The stability of such systems can be analyzed through complex eigenvalue analysis, through which we present a squeal noise criterion to be minimized as a computationally expensive black-box function. The computational domain is discretized through isogeometric formulation for its advantages in optimization and superior approximation properties which are well studied in structural dynamics. To be computationally efficient with the expensive black-box function, we defined the optimization based on efficient global optimization scheme in the context of multi-objective optimization, with the integration of Isogeometric design-through-analysis methodology. As gradient information is hard to access for such black-box functions, in addition to the presence of constraints, we relied on meta-heuristic approach as a more generic strategy for realizing optimization of such functions in multi-objective context. As one such scheme with its own advantages was observed to provide lack of resolution to define expected improvement (EI) with a single reference value, we propose a multi-reference acquisition strategy which can be defined through a fast and efficient algorithm with fewer adaptation to the existing scheme. Results show the efficiency of this approach for our applicative example, which can be extended to other such applications as well. [ABSTRACT FROM AUTHOR]