The most immediate consequences of Executive Order 9066 was to ensure that the Roosevelt Administration asserted total authority in wartime. The internment of people of Japanese ancestry represented to what lengths the American government would go to ensure that there would be no possibility of treason during wartime. The consequences of the Executive Order was also to clearly demonize the Japanese as "the other." Even if the Japanese it targeted had nothing to do with anything subversive, the consequences of the order was to clearly identity "the other" as a Japanese enemy.
Fueled by the propaganda that served to embolden those in the position of power, the long term consequences of the Executive Order was to reduce the moral stature of the United States in fighting the war. While the need to attack and take action against Hitler was absolute, historical scholarship has revealed how the issue of Interning Japanese during World War II took away from the ethical imperative of the war's cause. From a moral or ethical point of view, the Internment of the Japanese on discriminatory grounds is in the same ballpark of the Nazi politics of discrimination. The experiences of those who were interned under Executive Order 9066 have eerily uncomfortable parallels with those who were arrested and held by the Nazis. It seems that this decrease in moral stature would be another consequence of the Executive Order. History seems to echo this, as President Ford revoked the order and President Reagan ordered reparations to be issued to former internees.
The consequences of this executive order were felt exclusively by the people of Japanese descent (we cannot properly call them Japanese Americans since the issei were not allowed to be American citizens).
The people of Japanese descent living on the West Coast were, of course, interned. This was the first impact on them. They were taken away from their regular lives and were put in prison camps. This was very difficult for them as the conditions in the camps were generally quite poor. In addition, the emotional stress was very difficult for many of the internees.
A second impact came about because of what happened to the property of most of the internees. In most cases, their property had to be sold to whoever would buy it for whatever “fire-sale” price they could get. This led to a massive loss of property which made it hard for many internees to put their lives back together after the war.