TOM..
      I totally agree with you. You do have an assembly drawing that gives
  you the reference designation of a part and on a production job, with all
  the automation and transfer of information from a common database,
  who cares!!!  In many cases, especially with high density SMT assembilies,
  you cannot put the ref des anywhere near the part, which only adds to the
  confusing. The MIL-STD IEEE Std 200 para 8.1, states that ref des must be 
  on the PWB except: "Where space limitations preclude such marking".
     That being said, our circuit engineers, inspection and test/rework
  communities use them extensivly during the prototype/pre-production phase
  of a job and I would attempt to please them. Once passed that, I would 
  delete them.            
                                              Regards,
                                                        Bob Vanech