Cite keys can be generated automatically using the Cite Key Preferences. Note that the BibDesk will only automatically generate a key when all the necessary information is supplied.
If you want to force a cite key to be generated, for example when you do not have the autogeneration feature turned on, or you know you do not have the full bibliographical information, you can choose "Generate Cite Key" from the "Publication" menu (keyboard shortcut ⌘K), or from the action menu in the Editor for the item.