Shadow Killed enemies are still detected
Solution 1:
I searched for an answer to this and discovered similarly confused players.
Odd Shadow Kill Experience
However, I did find one possible explanation. According to IGN, you can't Shadow Kill someone in a conversation unnoticed. This makes me wonder that, as the NPCs wander, they expect to "check in" with other NPCs. If you Shadow Kill one and the other NPC can't "talk" to him or her, maybe they get alarmed.
IGN: Shadow Kill