Q: If you have the Shield Mastery feats that grant you active defense while using a shield, is it possible to stack the active defense of a shield in each hand?

Only if you have Improved Shield Bash 5. You could fight with a shield in each hand using Two Weapon Fighting, but you would not get to stack the bonuses for the ‘weapon hand’ shield (and would lose the off hand bonuses if you attacked with your off hand and did not have Improved Shield Bash 1).

Q: Do the Defense bonuses from Shield Mastery count for purposes of figuring out if an opponent hits your shield or not?

Yes. All defense bonuses from Shield Mastery count for purposes of figuring out if they hit your shield or not.

So if you have a heavy shield, Shield Mastery 1, 3, 5 and 6, and take a starndard action to protect yourself with the shield, the difference between your full defense and your shieldless defence is 3+1+1+1+4 = 10.

Shield Mastery 6

The advantage of Shield Mastery 6 over the standard defense action is that you can still make Attacks of Opportunity. Standard defense does not allow you to do this.