It was determine that there is no bug that is for sure. The numbers change after many seconds for me.
Kinetic and energy resistance is improved. This is a very fun PvE ship with the 3 consoles. It does not have much use in PvP with the 3 consoles removed. It would of the bonus from using them was a little better especially Kinetic.
It's a little confusing because the Set description does state Hull Plating:
While they may not be equipped on the standard Odyssey Cruiser or any other ship, the 3-piece set bonus decreases the recharge time of all Odyssey console abilities. It also improves your Starship EPS, Starship Hull Plating, and Starship Armor Reinforcements Skills. Finally, this bonus also slightly increases your Odyssey's Turn Rate.
I can see where some might think that means additional Hull, but Hull is not the same as Hull Plating.