From a gameplay standpoint, it's so beefy to ensure that blasting the reactors is the most practical way to take it down.
In-universe though, well we know that Shivans can make some ships unbelievably tougher than others of similar size (see the Lilith), so it's possible they just make some more of their more critical ships with more expansive materials, while everything else gets mass-produced on the cheap (including the Saths). I mean if you plan on making just a handful of Lucis to cover your planet glassing needs vs. the hundreds of Saths required for your star-blasting needs, the extra-strong armor per Luci is not gonna cost you that much, so why not add some extra-insurance to back up the shield.
Or maybe it's the other way around, Lucifers used to be pretty cheap, then their victims started focus-firing on them, so they beefed up the armor, and when that still wasn't enough they slapped the shield on.
As for "modernizing" the Lucifer - making it more than an extra large target, well some extra turrets would certainly be nice, preferably with more modern guns. It certainly should be using the LRed, or FSPort's version of the Super Laser as its main guns, plus maybe some custom beam type for the side beams, which would at least put it above the Ravana in firepower.
If you can't add more guns, then you probably want to make them extra-resilient and use stronger weapons with extended range, like AAAs, flak guns and better missiles.