No, missiles don't inherit the ship speed, but as they are dumbfire getting in close quickly could allow three direct hits, then a quick escape.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.
As for the Gauss... my Courier cannot handle three. I tried. I do have two, plus two large AX MCs and a flak on my Krait - I'm just looking for something different to try out.