For the simple reason that shoes, like clothing and other personal property, were a resource the camp system would seize and redistribute back to Germany. In the case of shoes, there were shortages of shoes within Germany as the war increasingly ate up stocks of leather and rubber. The use of ersatz synthetic materials such mipolam or cellulose caused a degree of civilian grumbling. The shoes of murdered Jews or other KZ inmates was a way to feed back prewar-level quality shoes back into the Reich's civilian economy. This expropriation and redistribution system grew larger and more sophisticated as the camp system evolved. The area of Auschwitz nicknamed "Kanada" became infamous in survivor memories for being a site of looting the valuables of murdered Jews. Of course, the SS often had the pick of this loot, including shoes, and there was a great deal of corruption in this process.
Jews who survived selection or other inmates tended to receive camp-issued wooden clogs. These too feature heavily in memories of the Holocaust, especially the "click-clack" sound they made as KZ inmates increasingly were used to repair bomb damage. Corruption within the camp system did also mean some of the looted shoes found their way back into the camps on the feet of various Prominenten or Kapo prisoners in charge of other prisoners.
So asking Jews to remove their shoes was not just about ritualized humiliation or to ease the extermination process, although those were factors operating in the Holocaust. The wider Nazi mentality was that all Jewish wealth was stolen so they held no moral qualms about taking every last bit of personal property from the Jews they murdered, including what was on their victims' feet.