The gun the hit-man Duke (portrayed by Frank Webb) uses to kill Edmonds (portrayed by Albert Paulsen) is a revolver with a silencer attached. The silencer would not work in this scenario, because in order for a silencer to work, it is necessary for the sound and gas produced by the gun remain inside the "closed system" of a semi-automatic, in order to be stifled and dissipated by the attached silencer, instead of escaping from the open cylinder of a revolver.
When Willie punches McGarrett in the cellar, the sound effect occurs significantly afterward, practically when McGarrett is falling into the boxes.