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The Kitaev honeycomb model has attracted significant attention due to its exactly solvable spin-liquid ground state with fractionalized Majorana excitations and its possible materialization in magnetic Mott insulators with strong spin-orbit couplings. Recently, the 5d-electron compound H3LiIr2O6 has shown to be a strong candidate for Kitaev physics considering the absence of any signs of a long-range ordered magnetic state. In this work, we demonstrate that a finite density of random vacancies in the Kitaev model gives rise to a striking pileup of low-energy Majorana eigenmodes and reproduces the apparent power-law upturn in the specific heat measurements of H3LiIr2O6. Physically, the vacancies can originate from various sources such as missing magnetic moments or the presence of nonmagnetic impurities (true vacancies), or from local weak couplings of magnetic moments due to strong but rare bond randomness (quasivacancies). We show numerically that the vacancy effect is readily detectable even at low vacancy concentrations and that it is not very sensitive either to the nature of vacancies or to different flux backgrounds. We also study the response of the site-diluted Kitaev spin liquid to the three-spin interaction term, which breaks time-reversal symmetry and imitates an external magnetic field. We propose a field-induced flux-sector transition where the ground state becomes flux-free for larger fields, resulting in a clear suppression of the low-temperature specific heat. Finally, we discuss the effect of dangling Majorana fermions in the case of true vacancies and show that their coupling to an applied magnetic field via the Zeeman interaction can also account for the scaling behavior in the high-field limit observed in H3LiIr2O6.