1796, "to make the sound of a cork being pulled from a bottle;" imitative. This was the main sense through most of 19c. Meaning "to hit, strike" is attested from 1943 (perhaps a variant of clonk). Related: Clunked; clunking. As a noun, in reference to the cork-pulling sound, by 1823.
"anything inferior," 1940s, agent noun from clunk (v.), probably in imitation of the sounds made by old machinery. Specific sense of "old car" was in use by 1936.