Assuming there is no further interaction a player can have with an enemy after it dies, I do think a good approach is to queue_free (delete) the original enemy scene, and instantiate a separate cosmetic "death effect" scene (such as a particle effect or animated sprite) in its place. You would also be able to reuse this death effect for other enemies.
I wouldn't recommend attaching such a scene to the enemy, because then you would need to write code to deactivate the enemy's logic, collision, etc. when it would've saved a lot of time to just remove the enemy entirely. If the enemy is managing its own health and handling how it reacts to changes in its health, you can have the enemy scene itself instantiate the death effect scene at its current position right before it deletes itself.
