No problem!  The baggage you'll have to deal with as a ninja comes from the fact that the japanese ninja clans attacked the US, but the American clans were on the allied side.  This took a long time for the public to figure out, but ninjas were eventually allowed to join the Normandy invasion.  Obviously, you could also be on bad terms with your clan; ninjas in the setting aren't exclusively Japanese, though most are either from Japan or North America