We consider a standard microscopic analysis of the transport coefficients, commonly used in nonequilibrium molecular dynamics techniques, and apply it to the smoothed particle hydrodynamics method in steady-shear flow conditions. As previously suggested by Posch [Phys. Rev. E 52, 1711 (1995)], we observe the presence of nonzero microscopic (kinetic and potential) contributions to the total stress tensor in addition to its dissipative part coming from the discretization of the Navier-Stokes continuum equations. Accordingly, the dissipative part of the shear stress produces an output viscosity equal to the input model parameter. On the other hand, the nonzero atomistic viscosities can contribute significantly to the overall output viscosity of the method. In particular, it is shown that the kinetic part, which acts similarly to an average Reynolds-like stress, becomes dominant at very low viscous flows where large velocity fluctuations occur. Remarkably, in this kinetic regime the probability distribution function of the particle accelerations is in surprisingly good agreement with non-gaussian statistics observed experimentally.