Janus phoretic colloids (JPs) self-propel as a result of self-generated chemical gradients and exhibit spontaneous nontrivial dynamics within phoretic suspensions, on length scales much larger than the microscopic swimmer size. Such collective dynamics arise from the competition of (i) the self-propulsion velocity of the particles, (ii) the attractive/repulsive chemically-mediated interactions between particles and (iii) the flow disturbance they introduce in the surrounding medium. These three ingredients are directly determined by the shape and physico-chemical properties of the colloids surface. Owing to such link, we adapt a recent and popular kinetic model for dilute suspensions of chemically-active JPs where the particles far-field hydrodynamic and chemical signatures are intrinsically linked and explicitly determined by the design properties. Using linear stability analysis, we show that self-propulsion can induce a wave-selective mechanism for certain particles configurations consistent with experimental observations. Numerical simulations of the complete kinetic model are further performed to analyze the relative importance of chemical and hydrodynamic interactions in the nonlinear dynamics. Our results show that regular patterns in the particle density are promoted by chemical signaling but prevented by the strong fluid flows generated collectively by the polarized particles, regardless of their chemotactic or antichemotactic nature (i.e. for both puller and pusher swimmers).