If the Beam Cannons bypass shields, what is the idea of keep the shields? A strong attack is the best defense. Anyway, The Lucifer-class should be something special to the Shivan, lets just say, a fleet of +90 Sathanas cant be builded in 30 years... The Lucifer-class could be a Speacial operations ship or a scout ship... Something special, Anyway, is the same tha let say, Why the Sathanas dont have shields? or why any other ship have shields?, that is because those big shield system needs extreme power to work and keep them up. That limits the offence power, so lets wipe them out and add more offence power. The Sathanas is the best esample.
Think this... in the Ancients records, they say "When the destroyers came for us, we attacked. Never had we been defeated. They were like the others: strange, hideous, resisting, fighting. Only these were not like the others: They did not die."
And more exsactly, the part "They were like the others: strange, hideous, resisting, fighting" others what?, the Shivan are the only race that the Ancients meet, so when they say: "When the destroyers came for us, we attacked." they refers to that class of destroyer... Could be the Lucifer-class or... Could be a Sathanas class which shields, the Shivans at that moment, the shivans could using shields on his super destroyers at the cost of firepower. of cource, the beams not even exist.
Well just two thing: The Lucifer Class is old ship or a "special Class", the Beams cannons rendered the Shield tecnology on big ships obsolete.