What a good question! Guzeman spends a lot of time showing us the various homes in the novel, so much so that we can reasonably suspect they are important. In fact, they are metaphorical extensions of the characters who live there and the life circumstances they face.
Thomas's dark and dreary apartment certainly seems to sum up his life. The light in his life - his painting, the women, the money, etc.- has gone out by the time we see him there. His is a life of darkness and things hidden.
We see Alice and Natalie's childhood home in several incarnations. Alice's childhood memories of her home are filled with happiness. When she becomes pregnant, she plans to raise her child there. Then a violent storm sweeps in on the night of Agnete's birth, and the house becomes a different place. Natalie is in control now and she makes sure Alice thinks the home is damaged beyond their ability to repair it, an allusion to the relationship between the sisters. Still later, the house is being rented by a family. It is in disrepair, but still holds treasures like the piano and Thomas's painting. Like Alice, Natalie, and Thomas, it holds its secrets close.
When they move from their childhood home, Alice and Natalie buy a large, old house in a small town in the midwest. This house has a rather Dickensian feel to it. So does the relationship between Natalie and Alice. Natalie is cruel to Alice, who suffers silently and becomes nearly a recluse. Saisee and Phinneaus see what's going on, but neither steps in to help until Natalie dies unexpectedly. This house also hides secrets - another painting by Thomas, Natalie's communications to Thomas, information about Agnete, etc.
Horrible memories or secrets follow the characters wherever they go. Any of these houses could have become a happy home, but because they are a reflection of the people who live in them, they are anything but happy.