mnftg64, the Lucifer in FS1 was set with an invulnerable flag by the mission designers. That is the only difference. It's an in mission, FREDded, "invulnerable" flag. Except in the last mission (Good Luck), obviously. There is no "special shielding" of ANY kind built into the ship, although I'm sure someone could conceivably add sheath shielding to the HTL Lucifer and set the shields powerful enough that only beam cannons, and not fighter weapons, can penetrate it.
That's why if you make a mission in FS2 and slap a Lucifer class into a blank mission and shoot it, you'll do damage. Canonically speaking, [V]olition never had a Lucifer class in the FS2 campaign (only the heavily armored Sathanas) so they didnt bother to make the FS2 Lucifer actually have shields penetrable only by beam cannons, hence your confusion.