The ancients weapons could even have not done anything to ships hulls, you have to figure fighter hulls can widthstand multi-kiloton blasts; maybe Ancient weapons weren't up to the job
While it's not an iron-solid conclusion, the fact that (A) the Ancients' civilization was geared for conquest at the time that they encountered the Shivans, and (B) they had the technology and energy generation ability to create the Knossos at least suggests that their weapons would have been superior in power output to Terran/Vasudan weapons.
Also the comments about irony in the final Ancients cutscene make a lot less sense if the Ancients could not have destroyed the Lucifer anyway, even if it didn't have shields.
Keep in mind the Shivans may not have used the same tactics against the Ancients as they did against the Terrans and the Vasudans. Since the TV were able to develop defenses and offenses against shielded ships rather quickly, it was to the Shivans' advantage to deploy capital ships to offset the balance of power in their favor. Since it seems as though the Ancients never developed any effective weapons against shields, the Shivans may have just deployed fighters and the Lucifer and sat back and massacred the Ancients, while holding the rest of their fleet in reserve.
