To answer my own questions, summarizing some threads on the Apple developer forums:
Yes, if you want to sell individual issues, you must have a (non-consumable) IAP set up for each.
Last fall, "Transporter" was added to iTunesConnect to allow upload and management of IAPs from the command line. See WWDC12 slides. You can find the user guide and the XML spec at the bottom of the "Manage your applications" page in ITC.