You're right in discussing the CIWS as the last-ditch defense for a warship (and land targets--these days some land sites are also equipped with CIWS systems). However, it is not the only last-ditch defense. There are also electronic jamming and chaff-type physical jamming systems which operate to the last second before impact. Also, the Aegis system isn't the only ship-defense working for the US Navy--if there are carriers around, then the E-2D and carrier fighters will also form the first outermost layer of air defense (which may extend out to several hundred miles, far greater than the range of any SAMs).