(From A Terrible Kindness by Jo Browning Wroe, Part II Cambridge Choir, chapter 14)
'Where are we going?'
'Song room,' says Martin
'Not the chapel?'
'Choristers go there for evening practice and then evensong, but it's here in the morning.' It's a small, very ordinary room, with cream walls and rows of benches. 'Probationers sit over there.' Martin points to the far corner and gently presses his back.
Even though William knows he'll eventually become a chorister, a pebble of disappointment plummets the length of him.
I take the bold phrase to mean "he is overwhelmed by dissappointment". I don't think it's an idiomatic phrase – I can't find any corresponding idiom.
Best Answer
This is a metaphor and poetic language. You are right that it's not an idiom you will likely see anywhere else.
Most simply, the author means that he is disappointed. However, he is describing the physical feeling of disappointment as it travels throughout William's body. We, as readers, should imagine a small stone - a pebble - being dropped through our bodies as if they weren't there. How would it feel? Probably cold, and strange, and maybe leave a feeling of emptiness. It would fall quickly, because it's a stone, but the hole it leaves would just be a small one, since it's only a pebble. (Which gives the sense that this isn't an overwhelming disappointment, just a regular one.)
This author's choice of metaphor likely alludes to more common idioms such as:
As you can see, feelings of stress, anxiety, embarrassment, etc. are often portrayed by something falling or something heavy. A pebble is a small way of saying the same thing.