No new insights, haven't been doing anything with Moo since then, and just knowing that there is a BD progression with the missiles is enough to satisfy my curiosity for now; explains my experiences.
Re. Antarans and Missile Evasion: I only now checked and the fleet-wide jammer is already there, on the small ships of all things. So I'm a little at a loss.
One option would be to put the jammer on the Fortress, as it's really the main enemy. Instead of just getting the +30 from the secondary effect, it would get the full thing, requiring scanners/sensors and ECCM. If you need to make room, you can remove the Energy Absorber and, if you prefer to keep things effectively unchanged, increase its hitpoints by 25% or something.
On the other hand, I kinda dislike the fact that the Fortress is so much more important than the fleet there, so that if you crack that, you're basically done, and round 3, when everything finally uncloaks, is really just mopping up, so I don't like upping it directly even more, especiailly in ways that don't up the rest of the fleet.
So another idea would be to put some kinds of Jammers on the larger ships, Harbingers and/or Interdictors.
In the end it's not really that important an idea, but something maybe worth keeping in mind if you ever up the torpedoes.