For writers, everything has been done under the sun. Every story. Every trope. Every character. They have all been written into oblivion. An affair could be creatively lazy, but it doesn't have to be. It depends on one matter - execution. Like Nate said, writer bias will probably play a role. A NaruSaku shipper will more than likely do characters injustice. They might spin the web to try and justify that the affair is correct without fault to Naruto or Sakura; however, in the right hands that doesn't have to be the case. But it will more than likely be the case.
The challenge in writing comes from being emotionally involved with your characters and not being emotionally involved at the same time. It sounds oxymoronic but it isn't, I promise. An author has to understand the psyche of their character while also being able to make plot choices based on the good of the story, not the good of the character. I can't tell you how many times I have been given a story meant to be dark in some fashion, only for the author to have gotten so attached to their character that they abandon the story's integrity for the perfect ending with all loose ends tied up, etc.
I wholeheartedly agree with this.
As a reader, I personally think affair fics are really enticing when done well! One author who writes HHr is writing a spectacular fanfic. It's one of my favorite fics actually.
They can definitely be creative, but yeah, a lot of authors try to justify the affair by having the other partner have an affair as well. Those type of fics get repetitive in fanfiction.
As a writer, I personally don't feel comfortable writing an affair fic. I've thought about writing one just for the sake of writing one, however I simply would not feel comfortable and morally right if I were to write one.