Wholesale costs will display in the Merchandise Summary report for products that have been added to inventory via a Purchase Order and have "Is Inventoried" set to YES on their Products page. The wholesale cost in this case will be retrieved from the PO.
For products that have only been added via the Retail > Products (not a PO), it is required to be set as "Is Inventoried: NO in order for the Wholesale cost to display in reporting. The wholesale cost in this event will be retrieved from the item's product page.