Yes, the ducks are important. For Holden, the ducks represent continuity, something that he needs in his life. When he goes to Central Park to look for the ducks, he has a question about where they go in the winter. Technically, what really fascinates him is that they come back in a very reliable way.
Holden is suffering from grief over the death of his brother. He is isolated from society feeling unable to make a true connection with anyone. Holden finds everyone around him to be phony.
The ducks in the park comfort him, make him feel safe in the belief that there is something reliable in life. The ducks always come back, you can depend on it. This provides Holden with comfort.
The ducks need to rely upon their instincts as the winter approaches. Holden is unconsciously equating this plight with that of adolescents who are confronted with the gray convoluted world of adulthood. He only supposes two possibilities for these ducks. They can either follow their instincts and fly south, or someone in a truck comes to take them away. This is his quandary. He feels no "sense" of where to go or what to do. So he fears that men in trucks will come to take him away. He does end up in a facility of some sort to care for his psychological problems.