Been struggling with this in my current "Ninja" playthrough.
One of my least favorite / most reproducible encounters is with the zombie cop sitting on the floor behind his desk in the video store/police station POI.
I can see his big blue butt by looking between the legs of the desk, but the game treats that piece of furniture as solid so I can't shoot him.
If I enter the room, no matter how quietly, he will wake up and aggro on me as soon as I reach the appropriate spot on the floor which, by the way, occurs before I get a clean line-of-sight to pop him while he's still sleeping.
"Best" solution to that jerk? Demolish the desk with my axe, then shoot the cop with my crossbow.
That one encounter, right there ... that's enough to leave me feeling like the game is fighting against itself and losing.
Devs want players to feel stealth is a viable option, but also feel the need to have encounter triggers that make stealth practically meaningless.