There are a few reasons, including the fact that AOE spells like Fungal, Storm, Parasitic Bomb, etc have significantly larger radii than Thors or Archons, the fact that the player can control where the AOE spells land, and the fact that casters usually have an arsenal of other powerful utility spells that they can use for different situations.
Thors and Archons are not going to wipe out “40 Mutalisks” unless the Zerg player stacks those Mutalisks extremely tight, and in the case of Archons decides to fly close to the Archons with that clump.
The Thor’s radius is 0.5. To contrast that with spells:
- Storm has a radius of 1.5, which covers 9x as much area.
- Fungal has a radius of 2.25 which covers 20.25x as much area.
- Parasitic Bomb has a radius of 3, which covers 36x as much area.
The Archon has a full damage radius of 0.25, half damage radius of 0.5, a quarter damage radius of 1, and a range of 3; so AOE damage spells both severely outrange Archons and still cover significantly larger areas.
Anyway, a single AOE spell is usually worth the attacks of several AOE units on its own.