If a player's deck runs out of cards due to an effect (such as forced discards or Sanctuary destruction), the rulebook does not specify that a Sanctuary is destroyed as a result of the deck running out of cards.

From the context:

• When a Sanctuary is attacked after being destroyed, "the defending player removes the top card of their deck from the game, face-down (it does not go in the Discard Pile)" (page 20).
• There is no mention of what happens if the deck is empty when this effect occurs.
• The destruction of a Sanctuary is only triggered when its Aegis counter reaches zero (pages 11, 20).

Summary

A Sanctuary is destroyed only when its Aegis counter reaches zero, not when a player's deck runs out of cards. The rulebook does not specify any additional consequences or destruction triggers related to an empty deck during effects such as forced discards or Sanctuary destruction.

Source: pages 11, 20.

Source: Core Rulebook (pp. 11, 18, 20, 22, 26)