For purposes of Saturation Salvo, If a Kihraxz Fighter equips the Vaksai title, is the squad point of their equipped missile the full value, or reduced by one?

As an example, would a missed Concussion Missile be worth 4 points and trigger against ships with 3 agility... or is it now worth 3 points, and only triggers against 2 agility ships?

(edited for horrid spelling errors)

Since Vaksai reduces the squad point cost of the upgrades you use the modified cost.

Yup. Your Cruise Missile with Vaksai costs 2, not 3.