Even though I'd love to believe that the Lucy's shields are invulnerable to beams, I am afraid it can't be.
Why?
The reason is simple: if this ship would've been invulnerable to conventional weaponry AND beams, then the Shivans would've built a huge Lucifer fleet instead of a Sathanas fleet.
Let's assume that (since the Colly is the size of 12 Lucys and a Colly is, for instance, equals a size of a Sathanas) - being really pessimistic - that you can build 8 Lucifers on the "price" of one Sathanas. If so, the Shivans could've had a fleet of 640 invulnerable ships instead of the 80 Sathanii. It is clear that the Shivans would've built the Lucys - but they didn't. Thus it is proven that the Lucy isn't invulnerable to beams.
Note: It IS possible that the Lucy needs some special resources the Shivans lacked at the time. But this is unlikely, considering the probable size of the Shivan empire and the way the canon campaigns go.
I'd think that either the Sath-fleet was older than the Lucy one, And/or that that the Sath's were specifically sent there for collapsing Capella for *some* reason, and thus battlereadiness wasn't really prioritized...
As for reasons, the "Shivans!"-mod has a funny explanation

.
We've been over this before.
Fact: the GTVA build the Colossus to defeat any other Lucifers.
Fact: the Lucifer has shields.
Fact: in order for the Colossus to defeat a Lucifer, it must pierce the shields.
Fact: Beams pierce shields on a smaller scale.
Fact: The Colossus has beams.
Therefore: The Colossus could pierce the shields of the Lucifer with beam fire.
Fact: bombs were the most damaging anti-cap weapons GTA/PVN had.
Fact: bombs have a very minimal shield damage modifier.
Fact: shields regenerate the more damage, the larger they are.
Fact: beams don't have such a puny shield-multiplicator.
Thus, I'd assume it as a valid guess, that "the Colossus being designed to thwart another Lucifer attack" could mean just that it has enough beam armament to overcome the regeneration rate of eventual Lucifers' shields.
...though I have to admit I'm biased here - I actually never realized that AAA-beams were piercing my shields while first playing the campaign.
Furthermore, I'd assume the Shivans to NOT simply have sit on their hands, doing nothing research-wise during the last 8000 years - and neither do I think it believable that the GTVA should be that easily able to catch up on that!
And also, I'd like to have
effective capship-shields which can't just be pierced... It'd add an additional level/layer to capship battles.