We develop a new model, to our knowledge, for the many-body hydrodynamics of amphiphilic Janus particles suspended in a viscous background flow. The Janus particles interact through a hydrophobic attraction potential that leads to self-assembly into bilayer structures. We adopt an efficient integral equation method for solving the screened Laplace equation for hydrophobic attraction and for solving the mobility problem for hydrodynamic interactions. The integral equation formulation accurately captures both interactions for near touched boundaries. Under a linear shear flow, we observe the tank-treading deformation in a two-dimensional vesicle made of Janus particles. The results yield measurements of intermonolayer friction, membrane permeability and, at large shear rates, membrane rupture. The simulation studies include a Janus particle vesicle in both linear and parabolic shear flows, and interactions between two Janus particle vesicles in shear and extensional flows. The hydrodynamics of the Janus particle vesicle is similar to the behaviour of an inextensible, elastic vesicle membrane with permeability.