If you delete a "to be hidden" folder or file when it is visible, in such a way that would normally send it to the Recycle Bin, then it will indeed be sent to the Recycle Bin. To keep your "to be hidden" folders/files from going into the Recycle Bin instead press Shift when clicking on Delete (or pressing Delete) to delete a file or folder. This deletes the file/folder without sending it to the Recycle Bin.