Hydrodynamic interactions play an important role in biological processes in cellular membranes, a large separation of length scales often allowing such membranes to be treated as continuous, two-dimensional (2D) fluids. We study experimentally and theoretically the hydrodynamic interaction of pairs of inclusions in two-dimensional, fluid smectic liquid crystal films suspended in air. Such smectic membranes are ideal systems for performing controlled experiments as they are mechanically stable, of highly uniform structure, and have well-defined, variable thickness, enabling experimental investigation of the crossover from 2D to 3D hydrodynamics. Our theoretical model generalizes the Levine-MacKintosh theory of point-force response functions and uses a boundary-element approach to calculate the mobility matrix for inclusions of finite extent. We describe in detail the theoretical and computational approach previously outlined in Z. Qi et al., Phys. Rev. Lett. 113, 128304 (2014)PRLTAO0031-900710.1103/PhysRevLett.113.128304 and extend the method to study the mutual mobilities of inclusions with asymmetric shapes. The model predicts well the observed mutual mobilities of pairs of circular inclusions in films and the self-mobility of a circular inclusion in the vicinity of a linear boundary.