The allegory of mourning
The center of the story involves the psychopathology of children who, without supervision, decide terribly to not tell anyone their mother has died, choosing to pretend that everything is still fine. This means that they are asked to inherit the roles of their parents, without properly mourning them. The story can therefore be read as an allegory against cognitive dissonance, a sort of attempt to make people deal with the deaths of their parents in a healthy way.
The cement burial as a symbol
When the kids give their mother a makeshift burial in a bed of cement, they're also choosing to shove the entire question of death (not to mention the death of a mother) into a part of their mind they can willfully ignore. It's a symbol for cognitive dissonance, or the brain's ability to pretend things are different than the way one really knows them to be.
The incest as an allegory
There is a great risk between siblings in trying circumstances, especially the tragic death of parents. When the parents die, the siblings are forced to cleave so tightly to one another for emotional support, that the question of incest can sometimes be raised. The final scene of unabashed incest is a symbol for the way they enabled each other to indulge in fantasies. We know this because they get caught having sex at the same time Derek finds the rotten corpse.
The motif of the macabre
There are two deaths to start the novel, and then a semi-erotic relationship forms between siblings (ultimately becoming full-blown incest), not to mention there is the constant reminder of the dead body in the basement, the vile stench. By the way, their method of burial? Cover the body in cement. But as they quickly learn, that doesn't stop the body from rotting and emitting a smell. Little by little, an already dark story becomes creepier and more detached from normalcy. This is a motif signifying the dysfunction of the children's despairing situation.
Derek as a symbol
Derek represents the inevitable. In their glass castle, the children believe their rouse will work, but just as Julie inevitably begins wanting men instead of boys, so also the passage of time will be their demise. Derek finds the couple having sex, and he finds the body, a fulfillment of what should inevitably happen.
