“Look,” I show her, “there’s holes in my cake where the chocolates were till just now.”Clearly, Ma's words stuck with Jack, as he echoes her definition in the last line of the novel. In this case, the meaning of crater is simply the physical mark left in the absence of the chocolates. This is also part of Jack's meaning in the last line, as many of the the items in Room are gone. However, I think that he is thinking about much more than the missing items when he makes this powerful statement.
“Like craters,” she says. She puts her fingertop in one.
“What’s craters?”
“Holes where something happened. Like a volcano or an explosion or something.”
We can learn a little more about what Jack thinks about from how he uses it in this conversation with Ma.
“You know your heart, Jack?” “Bam bam.” I show her on my chest.In this case the imagery of a crater is used to represent something more abstract: the lack of Old Nick's capacity for feeling. Despite the fact that he instinctively associates the word "crater" with this idea, Jack doesn't seem to be totally sure that this is a proper use of the word.
“No, but your feeling bit, where you’re sad or scared or laughing or stuff?”
That’s lower down, I think it’s in my tummy. “Well, he hasn’t got one.”
“A tummy?”
“A feeling bit,” says Ma.
I’m looking at my tummy. “What does he have instead?”
She shrugs. “Just a gap.”
Like a crater? But that’s a hole where something happened. What happened?
By the end of the novel, Jack has a much better sense of how the world works, and is much more confident with his use of the word "crater." I believe that in addition to the missing items in Room, he is referring to it as a mark left by the events of the past 7+ years, starting with Old Nick building Room, and ending with their eventual escape. This really works well as simile, portraying Room as an empty shell where something significant happened, but is no longer relevant. By comparing Room to a crater, Jack acknowledges that he and Ma have moved on for good, and there is nothing left for them in Room.