Well, beams were developed to combat the Lucifer, not necessarily to be able to pass right through its shields. It was never tested whether beams would pass through the Lucifer's shields, so we cannot say. But to my mind, it only makes sense that beams would affect shields: both were, after all, originally Shivan technology, and secondly, if we leave aside the fact that fighter lasers in FS2 have been turned into little floating space-blobs for purposes of gameplay, there is no fundamental difference between fighter lasers and beam lasers. The only difference is the amount of energy involved.
In the case of a fighter, therefore, a beam should be able to overwhelm shields pretty quickly and penetrate to the hull even before the shield itself has fallen, but it will still be battering the shield too. In the Lucifer's case, it is harder to say whether its shields could completely stop beams and therefore have to be taken down first. The Lucy's shields were so extremely powerful compared to fighter shields that they may have been able to absorb all the energy bombarding them even from a beam cannon, but perhaps not. If not, then in that case the situation for the Lucifer would be comparable to that of the fighters, with the shield having to deal with so much energy that it couldn't catch it all and some would get by to the hull.