In 1383 DR Laduguer was destroyed, along with Deep Duerra, by the Morndinsamman, but I heard somewhere that he resurfaced later on. Is that supposed to be true?
We Don't Know for Certain, but he's probably alive again
A 3.5E sourcebook (The Grand History of the Realms) lists that Laduguer was slain in 1383 DR by the combined efforts of the Morndinsamman. This is the event you are talking about in the OP.
5E Lists Laduguer as a Lawful Evil Dwarven Deity in the Sword Coast Adventurer's Guide (page 22). And...
The Out of the Abyss Campaign Module lists him as the primary deity of Gracklstugh
This, by itself, would not be too strange. As a result of the aftermath of the Time of Troubles, The Sundering, and other events that have happened...Ao the Overgod has reinstated and resurrected several deities, and others thought dead have turned up again. That's the standing explanation for why gods that were not listed in prior editions are now listed in 5E. Basically...Ao reshuffled the Pantheon to make sure all the slots were properly filled in, and other gods just kind of...showed up again.
But, where the confusion truly comes from is in the D&D 4E Sourcebook "Neverwinter Campaign Setting." Here it states that the Duergar were not aware that Laduguer had been slain, and so Asmodeous began pretending to be him in order to accrue more followers and trick the Duergar into making pacts with devils. There is no indication that any mortals ever figured out that "Laduguer" was actually Asmodeous.
It is never explicitly stated one way or the other if Laduguer was resurrected or if mortals ever figured out that Asmodeous was pretending to be him. Laduguer simply appears in the SCAG as a valid Dwarven Evil Deity.
Thus, the question stands: Did Ao actually resurrect Laduguer (or was he 'not dead after all')? Or is "Laduguer" still actually Asmodeous pretending to be a Dwarven god?
There is one extra piece of information that implies (though it does not outright say) that Laduguer was, in fact, resurrected.
When Deep Duerra was slain alongside her Father...nobody ever took up her mantle. Asmodeous started pretending to be Laduguer, but no one was pretending to be Deep Duerra, she was simply dead. And yet, both sources in 5E that mention Laduguer as an active god also mention Deep Duerra as an active goddess.
So, we have the strong implication there that Because Reasons, Laduguer and Deep Duerra were resurrected, undoing the events listed in The Grand History of the Realms. No detail exists about how this would have happened...if they had secretly survived, or if Ao brought them back. But we do not know for absolute certain.
This is the closest thing we have to an explanation about why gods may be alive again with no real explanation.
Over and over, mourning bells have tolled for some of the deities of the Realms. Gods were struck down during the Time of Troubles, when the Spellplague wrought its destruction, and most recently when Netheril fell. Some deities have even been slain by mortals wielding impossibly powerful magic. When a god withdraws from a pantheon, divine magic tops flowing to the faithful, and miracles and omens a ociated with that god cease, that deity's priesthood lo es faith, and holy sites are abandoned or taken over by other faiths. To the deity's worshipers in the world, it is immaterial whether the god is truly dead or merely dormant- the consequences for them are the same either way. Yet, as recent events have borne out, a god who is gone might not remain absent forever. More than a few supposedly dead gods have returned and amassed a new body of worshipers. Indeed, the legends of some gods speak of a cycle of death and resurrection. As the Sage of Shadowdale once noted, "If the gods can grant the power to raise mortals from death, why do ye assume they should be laid low by it forever?"