It's my understanding that when a PC gets Deadly Accuracy, it only applies to one hit in an attack, even if you're using Two Weapons or Auto-fire.
However, I noticed in the NPC stat blocks, specifically the Master Hunter [Nemesis] on p.400, that his Deadly Accuracy damage bonus applies to ALL of his attacks.
What gives? Is this a mistake or is this meant to beef up the NPCs?
"Deadly Accuracy" for NPCs better than for PCs
NPC Stats are often simplified for the GM's personal use. Use it as you see fit.
What gives? Is this a mistake or is this meant to beef up the NPCs?
It's meant to simplify nameless NPCs so the GM has less to worry about.
Take a look at the Forsaken Jedi and Emperor's Hand stat blocks, particularly their entry for Force Powers. They can activate the basic power and a few upgrades for the cost of a single Force Point, where the PCs have to roll multiple Force Points in order to activate the base power + upgrades.
From Jay and Sam's answers on Episode 14 of the Order 66 podcast, this is 100% deliberate on their part, as they feel that the GM should be focused more on creating a fun & engaging session than micro-managing their NPCs.