I'm leaning toward the missile option. We already have AX Mcs, and I can envisage a niche for fast smaller ships in a supporting role with missiles. I fancy bringing my 750m/s Courier with three missile launchers to support a wing - missile flybys at max speed.
AFAIK missiles don't inherit speed of the ship they were launched from.
If you have Guardian Gauss unlocked, you'd be more useful to mount center hardpoint and one of the nacelles with it. Other nacelle should have flak launcher.
Or all 3 should be gauss, but that is quite wide hit spread, you will probably hit with only 2 of them. And they are hitscan.
The new anti-thargoid weapons are de-facto useful only for ships with enough spare hardpoints.
But because the flak is important and thermal vent beam very useful, it is probably only T10 that still has enough free hardpoints. But that ship is - diplomatically said - not very useful for direct thargoid interceptor neutralization operations.
Or for people who don't bother to unlock gauss - but I don't understand why, because you have to grind guardian mats for reloads (even more of them), so why not just grind for gauss - it won't take longer and you are in better position to fight thargoids than with advanced weapons.
My take on those new weapons is that unless FDev changes them, they won't be used a lot - even the missile that is better than MC.