I don't think the Lucy is invulnerable to everything. My take on the sheath shielding system:
Well my personal theory about beams piercing 'sheath' shields is that the sheath shield is basically an extremely strong shield that regenerates extremely quickly, and only a constant barrage of fire can pierce this shield. The damage needed is probably many, many Harbinger bombs exploding on the Lucifer all at once for about a minute constantly without break. Even a pause for a second or two will allow the shield to recharge to half or even full strength. All damage must be constant, with damage being delivered every split second.
The only way this could be done in the FS universe devised is the use of beam weapons. Beam weapons deliver a whole load of damage constantly for as long as the beam is fired at the targeted ship (in this case a Lucifer class destroyer). The beam will be able to pierce the shield after only a few seconds on the shield. Because the beam is always firing upon the shield, the Lucifer does not have enough time to recharge its shield. Thus, the beam will burst through, vomiting all its plasma on the Lucifer.