The cages are the physical, material, and psychological circumstances of the characters, primarily Hamid, but also Fajir, Mansur, and Rukiya.
Hamid himself thinks of the shop as a prison or cage from which he will never escape:
There were times when it felt to Hamid as if he had been in the shop always, and that his life would end there.
We are told that prior to meeting Rukiya, Hamid has rarely left the shop:
He spent his nights alone and never went out. It was well over a year since he had even left the shop, and before then he had only gone out with Fajir, before the old man
Hamid explicitly compares the shop to a pen:
The journey from bed to shop took a minute or so, and he never went anywhere else. ... His legs were misshapen from lack of proper exercise. He had spent the day in bondage, months and years had passed like that, a fool stuck in a pen all his life.
Hamid cannot even imagine any change in his life. He feels unable to return to his hometown:
The smell of the water suddenly made him think of his
father’s home. That town too had been by the sea, and once he had played on the beaches and in the shallows like all the other children. He no longer thought of it as somewhere he belonged to, somewhere that was his home.
He also cannot imagine moving to the city proper, being too trapped by fear:
He tried to picture people living in that dark corner of the city. His mind gave him images of strong men with cruel faces, who peered at him and laughed. He saw dimly lit clearings where shadows lurked in wait for the stranger ... But it was not only for the physical threat they posed that he feared the people who lived in the dark across the bay. It was because they knew where they were, and he was in the middle of nowhere.
He fantasizes about Rukiya, but all he can do is treat her favorably as a customer by giving her extra measures of whatever she is buying. She lets him know that this is not sufficient to win her favors:
‘You’re always giving me things. I know you’ll want something in return. When you do, you’ll have to give me more than these little gifts.’
So Hamid's material circumstances are a cage, trapping him in a boring job with long hours. Physically, the shop he lives in is a cage that he feels unable to leave. Psychologically, even when his encounters with Rukiya impel him to take nightly walks outside the shop, he is too fearful to imagine breaking out of his cage entirely. Above all, Rukiya makes clear that she expects more than he can give her, and his desire for her will likely remain unfulfilled.
Similar cages imprison the other characters too. Fajir is confined to his bed; Mansur is nearly blind, and is mocked for his sexual attraction to boys; Mansur's diatribe against Rukiya shows her to be trapped in a misogynist society; and Rukiya herself, like Hamid, has an unpromising job far from her own hometown. Ultimately, none of the characters seems able to escape from the cages that their circumstances have placed them in.