Direct CP violation in the hadronic charm decays provides a good testing ground for the Kobayashi-Maskawa mechanism in the Standard Model. Any significant deviations from the expectation would be indirect evidence of physics beyond the Standard Model. In view of improved measurements from LHCb and BESIII experiments, we re-analyze the Cabibbo-favored $D \to P\!P$ and $V\!P$ decays in the topological diagram approach. By assuming certain SU(3)-breaking effects in the tree-type amplitudes, we make predictions for both branching fractions and CP asymmetries of the singly Cabibbo-suppressed decay modes. While the color-allowed and -suppressed amplitudes are preferred to scale by the factor dictated by factorization in the $P\!P$ modes, no such scaling is required in the $V\!P$ modes. The $W$-exchange amplitudes are found to change by 10\% to 50\% and depend on whether $d\overline{d}$ or $s\overline{s}$ pair directly emerges from $W$-exchange. The predictions of branching fractions are generally improved after these SU(3) symmetry breaking effects are taken into account. We show in detail how the tree-type, QCD-penguin, and weak penguin-annihilation diagrams contribute and modify CP asymmetry predictions. Future measurements of sufficiently many direct CP asymmetries will be very useful in removing a discrete ambiguity in the strong phases as well as discriminating among different theory approaches. In particular, we predict $a_{CP}(K^+K^-)-a_{CP}(\pi^+\pi^-) = (-1.14 \pm 0.26) \times 10^{-3}$ or $(-1.25 \pm 0.25) \times 10^{-3}$, consistent with the latest data, and $a_{CP}(K^+K^{*-})-a_{CP}(\pi^+\rho^-) = (-1.52 \pm 0.43) \times 10^{-3}$, an attractive and measurable observable in the near future. Moreover, we observe that such CP asymmetry differences are dominated by long-distance penguin-exchange through final-state rescattering.