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Effects of bond randomness and site dilution are systematically investigated for the Kitaev model describing a quantum spin liquid with fractional excitations of itinerant Majorana fermions and localized fluxes. We find that, in the high-temperature region where the itinerant Majorana fermions release their entropy, both types of disorders suppress the longitudinal thermal conductivity while keeping the specific heat almost unchanged. This suggests that both disorders reduce the mean-free path of the Majorana fermions. On the other hand, in the low-temperature region, the other specific heat peak associated with the entropy release from the localized fluxes is suppressed for both cases, but it is broadened and shifted to the lower-temperature side by the bond randomness, while the position and the width are almost unchanged against the site dilution. Contrasting behavior is also found in the thermal Hall effect under a magnetic field; the half quantization of the thermal Hall conductivity is fragile against the site dilution, while it remains for the bond randomness despite the reduced onset temperature. We discuss the contrasting behavior from the stability of the topological nature by calculating flux condensation and Majorana excitation gap.