MIDI was always a specialist interface. Most Amiga users didn't have any gear to plug into a MIDI port and unlike many computers of the time the Amiga had great audio built in. For these reasons it made sense for MIDI to be an add on rather than included as standard, a decision that just about every computer manufacturer came to except in the case of Atari with the ST. Including Midi as standard on a Vampire board makes even less sense now than Commodore putting it on the Amiga would have.
Ironically the Amiga was an ex-Atari engineers baby whilst ex-Commodore boss Jack Tramiel and a lot of the engineers that Jack took with him had a hand in coming up with the ST. So what might have been if Amiga hadn't got out of the Atari development deal and gone to Commodore.
If the ever do a Vampire standalone aimed firmly at the Atari market then I can see a stronger argument for including MIDI as it has such a strong heritage there.