Destroy all artifacts, then Structural Assault deals damage to each creature equal to the number of artifacts that were put into graveyards from the battlefield this turn.
If a player controls an artifact creature with a shield counter on it as Structural Assault destroys all artifacts, a shield counter will be removed before Structural Assault deals damage to each creature. Unless that artifact creature has another shield counter on it, the damage won't be prevented.
Structural Assault counts the number of artifacts that were put into graveyards from the battlefield this turn for any reason, not just because they were destroyed by Structural Assault.