The ducks may relate to Holden's concern for his younger brother Allie. After a change in physical circumstances, the ducks disappear. Allie has died and also, in this way, disappeared. Holden's concern for the ducks may be an extension of his thoughts about Allie and, possibly, the afterlife Allie may or may not be experiencing.
This is one way to envision the ducks as being a part of a quite specific loneliness for Holden, stemming from the absence of his brother.
I feel as though the ducks represent Holden in two ways. Holden is very concerned where the ducks go during the winter. First, Holden wants to know if a truck comes to get them and take them to a place more suitable for them. This could show Holden's internal fear that someone will eventually come and get him and take him to where he belongs- a mental ward. Second, Holden wonders if the ducks choose, or know, to leave on their own. This, again, is like Holden. He left Pency early and has plans to run away from home as well. In both ways the ducks represent Holden. Regarding the loneliness aspect, Holden really wants to know if someone is looking out for the ducks or if they are on their own. This is another representation of the imagery related to Holden and the ducks.
Every winter the ducks disappear from the pond in the park, and Holden does not know where they go. He doesn't know anyone who does. These ducks are Holden. His loneliness, depression, and etc.are rooted in the fact that no one knows where he has gone--literally and metaphorically. He has vanished from school, but his parents don't yet know that. He has, however, been vanishing since Allie died. Look at all the schools and lack of achievement that he's experiencing, and yet not until he has the breakdown and is institutionalized does anyone know.