From my understanding, this card is now an instant ability that decreases all evil characters in play at the moment it is played, this would mean that if another evil character is added to play by some ability (say a banding from hand or as you said Unknown Nation) it would not be decreased.
This is different than an artifact like Crown of Thorns that is a continuous decrease that updates continuously.
I am fairly sure these are the current decrease ability rules. So to recap, No, Plague of Flies does not hit characters that enter play after it is played.