A warehouse can be deleted only if it was never used on any document (delivery note, receiving note, inter-warehouse, invoice, etc.). Otherwise, the warehouse needs to be deactivated (see the picture below). In that case, the warehouse cannot be selected on the new documents, while it will be still displayed on the old ones.
The warehouse with stock available can still be deactivated. In that case, the warehouse and stock will still be printed on the reports that display the stock (such as the Printout of stock in the Warehouse) or for inventory. If warehouse stock should be emptied, an inter-warehouse should be created or partial inventory.