I think the ordnance fix is more about giving better munition options, rather than fixing the old ones.
I don't think we are ever going to equip an advanced proton torpedo on any ship. ever.
However, the fix is to make the good stuff work better. Ion Torpedoes, for example, or Cluster Missiles. These can work out great. Additionally there still could be some unspoiled EPT that makes them even nicer. There is still plenty of information that we simply don't have yet.
About that... I would be curious to try Nera+AdvProtonTorpedoes+EM+Deadeye+Recon Specialist=39pts
Range 1 ring of kaboom!