With the critical effects of the upgrade does it ignore the shields and go right to the hull or do shields stop said damage?

It is simply damage...so if there are shields present, it will knock off a shield point.

From the FFG article: Star Destroyers!

"For example, the Victory I can equip the Assault Concussion Missiles upgrade. Then, whenever your attack includes a result on a black attack die, you can deal one point of damage to each hull zone adjacent to the defending hull zone. You can only trigger one critical effect per attack, so if you trigger the effect from your Assault Concussion Missiles, you won’t deal a faceup damage card to the enemy ship; of course, the exchange is that you will deal an extra two points of damage."

Shields still stop it.