I encountered the same issue, and did some testing.
Shadowing Beyond and Enduring Shadows are bugged. You won't get Sneak Attack and Backstab bonuses when using Arquebus weapon type - the only ranged weapon i tested, so possibly others are affected as well. However, Great Swords work just fine with those abilities - i don't know about other melee weapons.
[4.1.2] Shadowing Beyond + Backstab bug
in Pillars of Eternity II: Deadfire Technical Support (Spoiler Warning!)
Posted
I encountered the same issue, and did some testing.
Shadowing Beyond and Enduring Shadows are bugged. You won't get Sneak Attack and Backstab bonuses when using Arquebus weapon type - the only ranged weapon i tested, so possibly others are affected as well. However, Great Swords work just fine with those abilities - i don't know about other melee weapons.