Manson was sentenced to death, as was Van Houten (both sentences would be commuted when the nation temporarily halted all executions). She later got a retrial, because her lawyer dying should probably have resulted in a mistrial the first time. Hughes' body eventually turned up in a gorge. By this point, declaring a cause of death was impossible. Maybe it was in fact a flood. Or maybe it was the Manson family, dozens of whom remained free (and some of whom would go on to commit more murders).
During the filming of the Oscar-nominated documentary Manson, one of the Manson Girls claimed the family had in fact killed 35-40 people, and that "Hughes was the first of the retaliatory murders." After a prosecutor publicized this claim in a book, another family member got in touch with him to affirm that yeah, that was a family kill, no question about it. That's not exactly proof -- people like this love to take credit for every unsolved murder in the vicinity -- but as explanations go, it seems less weird than "Happened to die in a freak unrelated accident immediately after enraging a murder cult."