There’s a ton of missile targeting bugs and issues that I’d have hoped Gearbox would have fixed for the Remaster (especially since they had a modder giving input?). I don’t know which of these if any are fixed, but just from the top of my head the problems were:
Missiles aren’t targetable, ever. You can’t make them a valid right click target, and you can’t make them a valid band-box target.
Ships need the minelayer abililty (but not the ability to actually lay mines) to fire at missiles.
Ships only fire at missiles if they have not been given a direct attack order on something else, so you can’t focus fire and have PD going at the same time.
Beams cannot hit missiles.
And I’m sure there were more I don’t remember right now, but all of these are serious issues for any mod that needs missiles to be countered something that shoots at them.