This started as a response to
Kiki's brief essay on ninja and breakdowns, and why, since they are raised from early childhood to be killers, this should not be as much of a problem nor cause as much emotional distress as killing and battle do for modern day soldiers, who do not usually become trained killers until they reach adulthood. (Apologies if you can't read her essay, which is friends locked, but hopefully that summary at least gives you context for my essay.)
I think
midnightdiddle is right in some respects, but I also think, even for assassins raised since birth to be so, killing can be traumatic.
Even in a culture where reincarnation is the accepted religious belief and individual lives are considered less "valuable" than in a Judeo-Christian society and where hurting or killing a stranger causes little remorse, there is a burden of guilt in the taking of lives.
Even if they have come to see humans as objects and undeserving of sympathy, it does not change the fact that they themselves are human, and there are other humans to whom they must feel some form of closeness, be it family or friends. Even the most remorseless of serial killers, who have grown up torturing and killing animals, then graduated to killing people, usually have one or two shocked friends or acquaintances who can't believe such a nice guy could do something like that. When the assassin looks in the mirror, he will see a human being looking back. Biologically he cannot help identifying with his victims, at least a little.
Also, let's look at what exactly fanfic authors tend to portray as the triggers for their ninja character's breakdowns. It is usually not the simple fact of carrying out an assassination. Rather the triggers are usually something personal--the death of a loved one, a near-death experience of their own, an assignment to assassinate someone who reminds them of a loved one, a forced betrayal of their own comrades, etc.
Consider Hatake Sakumo, who, it could be argued, has had a traumatic breakdown that leads to his suicide. Here was a man, ninja since a very young age and evidently very successful as such, who is suddenly faced with a hideous decision: leave his comrades and friends to die and complete the mission, or save his comrades and allow the consequences of the failed mission to take hold. He chooses to abandon the mission, and as a result of his saving a few friends, many strangers die. His friends scorn him for his choice, and ultimately he ends his own life in shame.
His breakdown was not caused by killing enemies, nor even by being the ultimate cause of the deaths of those who were doomed by the mission's failure, but by the very personal emotional trauma of being abandoned by his friends, the very friends he had sacrificed the mission in order to save.
Now obviously the situation has more complexities than I am going into here, but still I think it illustrates my point: ninja are human, and it is their ties to other humans and the personal traumas that come from those ties that cause breakdowns.
I'm as guilty of writing ninja in fragile mental states as any other fanfic author, because it makes for good drama. But the traumas I've set on my characters have all been very personal ones: the deaths or near-deaths of loved ones, often with extenuating circumstances that leave my character feeling guilty for failing to save those hurt, severe injuries to themselves under torture or in battle, extreme emotional stress from caring for others who are in distress...
Yeah, I'm bad to my characters, and it makes for good fiction.
Anyway, I think it is important to remember these points in writing about ninja:
They come from a culture where human life is believed to be a renewable thing, where a soul goes around on the wheel of life and has opportunity to live again.
They are raised from a very young age to be comfortable with the notion that killing is part of living.
They also are raised to have loving relationships with their comrades, and to care for them. They have friendships and relationships like any other human.
The dichotomy of needing to be moral, good people within the context of their villages while at the same time having no compunction about killing enemies or assigned targets, is one which would inevitably lead to some degree of emotional stress.
So I think on the whole it is reasonable to postulate that ninja may suffer from varying degrees of PTSD and survivor guilt, and have occasional breakdowns. Not necessarily from the killing they themselves have to do, but from the death and suffering that affect them personally.