The first metaphor I see in the book is on page 2. It says that, as Kira watched her mother's spirit drift away, she could also see the "cindered fragments" of her childhood going up as well. Obviously, her childhood had not been burned and made into fragments. So this is a metaphor that is meant to show that her childhood is over.
Then, on page 27, we see Vandara say that Kira drags her leg around "like a useless burden." That's a simile because it uses the word "like" to directly compare two things.
As for themes, there are many, but you can argue that the most important one is the theme of how important creativity is -- that is why the Council of Guardians takes all the creative kids and controls them.
The theme of Gathering Blue is that persons with disabilities have value to a society. In the story the main character is a young girl who has a damaged foot that drags behind her body and causes her pain. However, she has been born with a gift of being able to weave. If it were not for this gift, she would have been put into a place to wait for death to come in the supposed form of forest beasts. However, in reality there are no beasts but a society of other people who sneak into the area and take the people to their home where they can live free of fear of having a disfigurement or disability or even old age.