Agreed - it appears that AISC 13th Edition no longer has 36 ksi values in Allowable Load Tables or Beam Charts. Yes, new W-shape beam should be spec'd as 50 ksi steel since that is what is available.
If you need to check for 36 ksi, you can use the formulae in AISC Spec to determine capacities, or if you are checking an existing beam, go back to the Green book (for ASD) or Silver/Blue book (for LRFD).