In this chapter, everything of worth is being stripped away from the Jews who own it by the Kapos and others in charge of the camps. Elie's shoes are brand new, and so therefore would be of great value to anyone whose shoes are in poor shape. Even if he didn't need the shoes himself, Elie's new shoes would be of value to the Kapo who could use them to barter for something he wanted.
Consequently, if these brand new shoes are covered in mud, it is difficult for anyone but Elie and Elie's father to know they are brand new and valuable. The mud, which would normally be a source of angst for Elie as his parents would likely be upset that he didn't take better care of his belongings, has served as a protector and a shield for Elie. He is able to keep his new shoes without conflict since the mud disguises their value.