We don't have a proof. And the Lucifer was deployed to make planets unhabitable. No, it isn't designed to "exterminate" a species. 
There are big problems with this statement.
Specifically, the only way to exterminate a species is to kill them all. Which the Lucifer is superbly equipped to do; it can glass a world from orbit, necessary to kill off a species with certainity, and because it does not rely on some form of expendable munition (read that: Harbinger bombs, the GTA could have wiped out Vasuda Prime just as thoroughly if they could get the bombs to the target) to do it, then the Lucifer can glass a planet hundreds or thousands of times, as many as is required to ensure nobody escapes. To claim this capablity was not intended in its design is
extremely tenuous.
Furthermore while there is no proof, the circumstantial evidence is very persuasive: technologically and numerically the Lucifer fleet is
vastly inferior to the fleet deployed in FS2. It seems probable it is therefore of an earlier vintage, and somebody cut it down to its current size. The only
known, and hence best, candidates for reason for deployment and inflicting losses on it are the Ancients. So no, it's not proveable, but it's the best theory out there.
On other subjects: given the Ancients had a much larger empire than the GTVA (this is what the GTVA believes however, and as an ingame source and not a :V: statement the possiblity of a fallible narrator comes into the equation), it makes sense they had a larger fleet. Given that they encountered
many sentient species, whereas the Terrans and Vasudans have only run into each other (and the Shivans), and unless their expansion was along a single line of jump nodes (highly improbable), they must have had a large fleet to push in so many directions at once. Assuming they made some attempt to hold the line at the edges of expansion against anyone who might wander in also implies a large fleet.
:V:'s statement that the Lucifer's shields would not hold up against FS2-era weaponry implies that the Lucy's shield worked on different principles from fighter shields. After all, lest we forget, the Lucifer spent 18 hours bombarding Vasuda Prime, and had to have made some kind of approach to it too. During which the PVN would have thrown everything they had at it. The resources of a world are not to be sniffed at; those of a homeworld, heavily fortified, are even less so. (Vasuda Prime had a direct node connection to Antares, which was often under Terran control or at least contested...and recall if somebody gets through to Vasuda Prime and drops a Harbinger we're looking at losing several hundred square kilometers just from the primary effects (blast itself) and an environmental disaster of momumental proportions.) The Harbinger, FS1's most powerful weapon, does damage equivalent to 2/3s of a Helios bomb. The Vasudans doubtless had their own super-warheads, or at least something as capable as a Tsunami, and no shortage of delievery platforms: this was their homeworld, they would have strapped weapons to anything that could move and stopped at nothing to deliever them to the target.
Yet the Lucifer shrugged it all off. This implies weapons below a certain power level cannot damage the Lucifer. If you could attrit its shields down to nothing like a fighter, then the PVN would almost certainly have managed it. However, the problem is worse than it appears even
then. The Vasudans have a known willingness to sacrifice their lives for the greater good (Anubis tech room entry, the HoL attempt to ram an explosives-filled cruiser into your home destroyer in FS1), and it is therefore certain that, in their darkest hour, someone (probably lots of someones) strapped the biggest number of bombs they could onto their ship and rammed the Lucy. An Amun packed full of Tsunamis or equivalent is going to make a boom at least equivalent to an FS2 Helios, probably more. (Nevermind an Aten loaded with nukes.) This didn't bother the Lucifer either.
Therefore it follows that it is worse than weapons below a certain power level being unable to harm the Lucifer. It was immune to that
type of weapon. There are two new weapon types in FS2: flak and beams. Flak, however, is merely explosives and projectiles delievered to the target in a new fashion. Beams are the only truly all-new weapon type. This
also makes them the only possible candidate for "FS2-era weapons the Lucifer's shields cannot stand up to".
This doesn't necessarily prove that beams beat all shields (though arguing they don't beat fighter shields is a lost cause for what should be obvious reasons), but it does prove reasonably well that they would beat the type of shielding the Lucifer used.
