"to hit hard, defeat decisively," 1941, British air force slang, of unknown origin, probably related to bombing; possibly echoic. Related: Clobbered; clobbering.
In late 19c. British slang an identical word principally had to do with clothing, as in clobber (n.) "clothes," (v.) "to dress smartly;" clobber up "to patch old clothes for reuse, conceal defects" (1851). The source of these seems to have been 19c. clobber (n.) "kind of coarse dark paste used to cover breaks in leather in old shoes," which seems similar to Gaelic clabar "mud," but OED writes that this is "hardly likely to be the word."