The Lucifer invincibility misconception
A common misconception among FreeSpace fans is that the SD Lucifer, the Shivan command ship leading the fleets that invaded GTA and PVE space during the Great War, is virtually invincible in all combat environments except for subspace, where its shields are not operational and subspace tracking technology obtained from research on Ancient artifacts effectively allowed a few Terran and Vasudan wings to bring this vessel down. Said misconception has sparked many ideas among the fans and consolidated over time, but claims from some of the game creators have provided new clues on the actual "invincibility" of this vessel.
In fact, old posts on the Volition Watch website clarified that the Lucifer was indeed impervious to FS1 era weaponry, but more powerful weaponry (and by this Volition didn't necessarily imply beam weapons) would have been able to penetrate its shields and therefore make the destruction of the vessel possible in environments other than subspace, where shields don't work. The Volition Watch website is no longer browsable but key posts from veteran community members who participated to these discussions can still be found on the Hard-Light Productions forums (e.g., 1, 2, 3, 4) and provide several details on how the information was given, as well as its implications.
Due to this concept being provided by FS1 game developers after the release of the game, and no requirement for it to be used in any tangible way in FS2 as the Sathanas juggernaut took the Lucifer's role as premiere Shivan threat, the concept itself remained stagnant even if it has all grounds to be considered canon for the FreeSpace universe. The fact that this notion was not widely used over time has contributed to consolidating the misconception by which the Lucifer would be truly invincible in all environments except for subspace, with some major implications on the FreeSpace plot itself and major influences on a multitude of fanmade campaigns.
The Lucifer and the Ancients
One of the main consequences of this invincibility misconception is the assumption by which the Lucifer pretty much single handedly vanquished the Ancient empire and bombarded planets such as the Ancients' homeworld with minimal resistance during the war between the Ancients and the Shivans that occurred eight millennia prior to FreeSpace. No canonical details on the matter are known, but considering that canonically speaking, Ancient technology was more advanced than that of the Terrans and Vasudans at the time of FS1, especially in the field of subspace, Ancient weaponry would have likely met the "strong enough to penetrate the Lucifer's shields" status, so we must look elsewhere for the true nemesis of planets colonized by the Ancients, though it's still possible that Lucifer-class superdestroyers did bombard Ancient planets at the time (it's worth noting that we don't know whether the Lucifer was a one-of-a-kind ship, however). The Ancients' fear of shielding technology described in cutscenes was likely a reference to the general characteristic of shield-equipped Shivan craft and their strategical advantage, and not a precise reference to the Lucifer's shields.
Beam weapons and shields
One of the main reasons, if not the main reason, by which the Lucifer invincibility misconception is so common may be due to the common belief according to which its shields would be easily penetrated and voided by beam weaponry. Therefore, community members may simply believe that FS2 era warships could outperform a Lucifer via beams, and damage its reactors directly, and as direct consequence, the notion by which conventional - and strong enough - weaponry could damage the Lucifer's hull is less common as it should. While beams are known for piercing through shields, it's worth noting that this is a bug in FreeSpace that the developers did not fix prior to release due to time constraints. It's possible that, canonically speaking, beams may be capable of piercing shields, but this has never been confirmed by Volition.
Fanmade plots based on Volition information
Despite the fact that misconceptions on the Lucifer's supposed total invulnerability from conventional non beam weaponry are very common, and campaign developers have had all the right to stick to that for their own storytelling purposes, it's worth noting that at least one fanmade campaign (the list is being updated) grounded its plot on the information provided by Volition on Lucifer shielding.
Please note that this is not a campaigns that got it right list, instead it provides general information and references on fanmade campaigns that used this knowledge in their plot setting. Also, please note that the following list contains spoilers.
Released in 2017 as a satellite project to Silent Threat: Reborn, the main fundament behind this campaign's concept was the notion by which some weapons, under the right circumstances, may have eventually damaged the Lucifer's hull in critical engagements that occurred during the Great War. Deneb III is a minicampaign that focuses on a desperate attempt by joint GTA and PVN forces to pass through the Lucifer's shields to inflict direct damage on its hull via a powerful bombing run, but the operation ultimately failed and the Lucifer proceeded its relentless run to key planets across GTA and PVE space.