With a population of 3,229, Korvosa is a large town. Supposedly it should lack 3rd-circle spells.
This is not the case.
Sure, many of Korvosa's wizards died last night. Death ward isn't a wizard spell, and wizards aren't known for their Strength scores. Most were weak to begin with and suffered age penalties, which begin at 35 and intensify at 53 and 70. Wizards that survived their first six seconds after being jumped by a shadow seldom made it through the next six.
Most of the spells that Korvosa's wizards prepared, not expecting a desperate fight in the middle of the night against incorporeal undead, were in the event pretty useless.
The median Korvosan wizard gets three or fewer spells per day. They have jobs to work; if a first-level wizard prepped combat spells with no plan to ever use them, who would pay them? And for what?
The fraction of Korvosa's wizards with combat spells don't fair much better - sleep will save you from a mugger in a dark ally, black tentacles will do much the same and with far more style, and neither will have any effect on a shadow.
But expeditious retreat, invisibility, beast shape I, dimension door? None guarantee survival, and not everyone had such a spell prepared. But for Korvosa's 3rd-circles, the odds weren't terrible.
And the teleport-capable Deans of the Academae were only ever in as much danger as they chose to be.