What is the upper deck on converted freighter long-hump 747s used for?
They have seats for couriers, same as factory freighters, but roomier.

Note: From the -400BCF type certificate:


  There are no provisions for the carriage of passengers. A maximum of 19 couriers can occupy the aft cabin of the upper deck as defined in AFM.





  
  Source: airplane-pictures.net


Above is the upper deck of a -400BCF (converted freighter).

And below on the left is an -8F. Also, note the foldable yellow ladder for access to/from the main deck.


  
  Sources: left: pbase.com; right: pinterest.com (original source unknown)