We analyze the structure of the surface states and Fermi arcs of Weyl semimetals as a function of the boundary conditions parameterizing the Hamiltonian self-adjoint extensions of a minimal model with two Weyl points. These boundary conditions determine both the pseudospin polarization of the system on the surface and the shape of the associated Fermi arcs. We analytically derive the expectation values of the density profile of the surface current, we evaluate the anomalous Hall conductivity as a function of temperature and chemical potential and we discuss the surface current correlation functions and their contribution to the thermal noise. Based on a lattice variant of the model, we numerically study the surface states at zero temperature and we show that their polarization and, consequently, their transport properties, can be varied by suitable Zeeman terms localized on the surface. We also provide an estimate of the bulk conductance of the system based on the Landauer-Buttiker approach. Finally, we analyze the surface anomalous thermal Hall conductivity and we show that the boundary properties lead to a correction of the expected universal thermal Hall conductivity, thus violating the Wiedemann-Franz law.