Apartheid
Gordimer doesn't have to use the word "apartheid" for us to know exactly what/when she's talking about in "Once Upon a Time." Her story is set in an affluent neighborhood full of selfish people in the late 20th century. Outside the neighborhood are riots by "people of another color" who are not allowed into the husband and wife's neighborhood unless they are "trusted." Those other people eventually do come into the neighborhood as outside events like "police and soldiers and tear-gas and guns...buses were being burned, cars stoned, and schoolchildren shot by the police in those quarters out of sight and hearing of the suburb" and widespread unemployment lead to the uprooting of a population. The husband and wife's inability, or lack of desire, to understand the plight of the Black people in their region and how members of their own white racial group were the ones who created this system of racial separation and concomitant unrest, despair, and deprivation encapsulates the brutal unfairness of apartheid in South Africa.
Racism
None of the characters says anything overtly racist in the story, but racism is still there, simmering just below—and, occasionally, just above—the surface. The "wise old witch" warns her son and daughter-in-law "not to take anyone off the street." The housemaid and gardener are Black, yes, but they are "trusted" and "highly recommended," which contrasts with all of the others. The housemaid criticizes other members of her race in order to set herself apart. The couple comforts themselves that they are not racist because their sign has a silhouette of a person who could be either white or Black. All of these examples contribute to the subtle racism that the couple possesses. They think they are not racist because they aren't openly aggressive about it, but they are fundamentally shaped by a sense of their own white supremacy such that every comment, every thought, and every action in the story is about keeping themselves safe from the dangerous, rapacious, threatening Other.
Fear of the Other
In the era of apartheid, which featured rigid separation of the races based on the complete codification of racial difference, white people and Black people had proscribed roles, areas, and stations, all of which were fundamentally different from each other. The white people in this story evince that deeply held fear of the "Other": Black people whom they believed to be trying to take their things and cause them harm. The while people see themselves as virtuous and beset-upon; they must keep their possessions and their loved ones set apart from the strange and hostile outsider.
Self-Sabotage
The husband and wife are concerned about the rash of burglaries and decide that they must shore up their home and possessions against the perceived danger of the shiftless Black itinerants coming around their neighborhood. They allow this fear to become an obsession to the extent that they render their house and property ugly, inhospitable, and, eventually, deadly. They sabotage themselves; the little boy dies not because of some faceless intruder but rather because of the couple's conviction that the Black people in the area are dangerous. They do not see that their own participation in a racist society perpetuates societal unrest and poisons their own sense of morality and ability to reason.
Loss of Innocence
The little boy is depicted as youthful, playful, and innocent. While his parents are erecting more and more barriers to protect their house from perceived danger, he is playing with his friends and delighting in books of fairy tales. However, that innocence is suddenly and violently lost when the little boy climbs into the barbed wire coils in a private game of make-believe and is cut to pieces. His death is a loss of innocence for himself; for his parents, who must "grow up" and realize what they've done; and, symbolically, for South Africa, as the whites there have perpetuated an insane and immoral system of racial separation that is not just bad for Black people but bad for whites as well.
The Home
The home in this story is fraught. It is supposed to be a refuge and a place of safety, but it instead becomes a site of imprisonment and horror. The outside world is to be kept out but seeps in instead—the husband and wife's racism, fears of the Other, anxieties, obsessiveness, and irrationality preclude them from fashioning what they intended. They hope for safety and security, but instead, they get death. The home does not need to be protected from the outside: the rot and the danger are within.
Fairy Tales
Gordimer plays with the structure and tropes and symbolism of fairy tales. Through her own "fairy tale," she reveals how those classic fairy tales are actually rather violent and rather grim; they sometimes have terrible fates for their heroes and heroines, and there is ambiguity as to whom we should root for. Similarly, the divide between fairy tale and real world is not as sharp as we might think. There are monsters in those tales, but there are also monsters in our real world. There are characters with foibles and flaws, as there are in the real world. There are villains in fairy tales, and there are certainly villains in the real world.