Co-based shandite Co$_3$Sn$_2$S$_2$ is a representative example of magnetic Weyl semimetals showing rich transport phenomena. We thoroughly investigate magnetic and transport properties of hole-doped shandites Co$_3$In$_x$Sn$_{2-x}$S$_2$ by first-principles calculations. The calculations reproduce nonlinear reduction of anomalous Hall conductivity with doping In for Co$_3$Sn$_2$S$_2$, as reported in experiments, against the linearly decreased ferromagnetic moment within virtual crystal approximation. We show that a drastic change in the band parity character of Fermi surfaces, attributed to the nodal rings lifted energetically with In-doping, leads to strong enhancement of anomalous Nernst conductivity with reversing its sign in Co$_3$In$_x$Sn$_{2-x}$S$_2$.