Spectral Armor is slightly more efficient than Zynthium against Energy weapons. This makes them suitable for ships designed for close combat such as cruisers and cutters: most short-range weapons are Energy-type such as the Burst Ray and Nova Ray, allowing your ships to survive longer and get less repair time.
Considering equal damage taken from Energy, Explosive and Projectile sources, Spectral Armor is actually less mass-efficient than Zynthium. It only works if you specialize your ships to only fight against certain types of targets.
To add insult to injury, the XP per health for Spectral Armor is also greater, setting your fleet up to be attacked by stronger ships.