A Subtle Knife is a hidden knife, which symbolizes scrutiny (defining ideas and judging between true and false), so what can be said of subtlety? Well for one thing, subtlety is Lyra's main skill, because she stays hidden from her pursuers. She is trailed by a torturous witch, and she is haunted on all sides by the problem of death and existential confusion. But, by paying attention to subtlety and nuance, she prevents herself from accepting ideas from those who are working to harm her.
The Subtle Knife is not unlike the alethiometer that the gang uses in their attempts to find truth. Just like she parses the intentions of those who would recruit her to their purposes, Lyra also parses truth and lies with the alethiometer. When John dies, Will is left to face Lyra's disappearance with only the help of what she used to provide to the group—the alethiometer (her truthfulness). In order to face the dilemma, he has to "face the truth," which is especially difficult, because it means facing the truth about John's death.
Death is the truth of the novel, from the looks of it. John doesn't need to check some sort of magic truth tool to see whether death is legitimate or not—he knows by lived experience that all people are mortal, and although the battle rages on, humans can disappear from the story without arriving at any hypothetical goal. The tragedy of life is on full display in the ending scene, because Will must simultaneously accept death and still hope that Lyra is alive somewhere.
