Like Hillerman's earlier novels, Sacred Clowns explores the various conflicts between Navajo and white culture. Also like some of his earlier novels, the book highlights conflicts among various Indian cultures, exploring how people's cultural backgrounds form their views of the world.

One of the major themes concerns the different ways that whites and Navajos view justice. White culture draws on the Judeo-Christian tradition that views justice as fitting the punishment to the crime. Thus, as Janet Pete, a half Navajo, half Scottish lawyer trained in the American justicial system, argues, when people commit crimes, they must be brought to justice and receive just retribution. Because Pete, having been raised off the reservation, is half Navajo by blood but not by culture, she does not understand the traditional Navajo position on crime that Jim Chee appreciates. This view argues another tradition of justice, that of restoring hozho, or harmony, after a crime. If Navajos harm another person, they must achieve justice not through retribution but through determining the amount of damage done and making appropriate restitution. In the novel, Clement Hoski, a Navajo grandfather, gets drunk and kills a pedestrian in a hit-and-run accident. He is a good man in every other way, the best sign of his goodness being his love for his abandoned grandson, Ernie, who suffers retardation from fetal alcohol syndrome. To provide restitution, Hoski is willing to pay the family of his victim every two weeks, and Chee, because he understands that sending Hoski to jail would harm Ernie and do the victim's family no good, saves Hoski from the retribution of American justice by refusing to arrest him.

A second theme concerns how different Native American cultural backgrounds lead to different understandings of the world. In Sacred Clowns, Hillerman explores in detail the cultural biases and blind spots that different tribes have for each others' cultures. When Chee and Pete view a kachina dance at the fictitious Tano Pueblo, neither Chee the more traditional nor Pete the more Americanized Navajo can fully understand the ceremony. Both are as much outsiders to Pueblo culture as are whites. When Chee, Pete, and Harold Blizzard, a Cheyenne, watch John Ford's movie Cheyenne Autumn with its Navajo actors playing Cheyennes, Blizzard does not understand the jeering reactions of the Navajo audience to the movie. His confusion is only partly because he does not understand the Navajo lines that the actors deliver; even when Chee translates. Blizzard, and Pete as well, lack the cultural backgrounds to understand the absurdities that the Navajo audience recognizes. Implicit in Hillerman's social commentary is the notion that people from different cultures cannot understand each other unless they strive to build bridges. Chee and Leaphorn represent an ideal in Hillerman's fictional world. While both grew up Navajo and understand their home culture, they also understand the white world in which they were educated and with which they interact as police officers.

An important subtheme in the novel concerns differing views of the land. Having a deep appreciation of traditional Navajo culture, Chee holds ambivalent views on appropriate land use. When he ponders the Navajo Agricultural Industries' success in irrigating what had been unspoiled desert to grow crops, he feels both pride and regret. He is proud that his Navajo forbearers had managed to save this property, and the water that irrigates it, from white landgrabbers; but he also looks with dismay at the destruction of its ancient beauty that the great spirit of Changing Woman had witnessed at Earth's beginning. Also, as an environmentalist, Chee writes a letter to the local paper speaking out against using the open pit of Jacks Wild Mine as a toxic waste dump, but Ed Zeck, a white expert on Navajo land use, views such a project as a sign of progress that brings needed jobs to the Reservation.