Jaheira most likely died from old age, including Neera from the Enhanced Editions. Half-elves live for 180 years or less, Baldur's Gate 3 is set in the same year as Descent into Avernus, 1494 DR, or maybe a few months or a year after it, and she was a young girl around 1347 DR, 21 years before the first Baldur's Gate game, but old enough to remember the Ten Black Days of Eleint incident in Tethyr, that would mean she expired a few years before Baldur's Gate 3, if no one killed her first.
Viconia is dead no matter if you've romanced her or not, and her non-romanced epilogue presents a continuity issue I can't find a way around. In her non-romanced epilogue, after saving the elven city Suldanessellar with Drizzt and his companions, she just mysteriously disappeared, no one knows what happened to her after she aided Drizzt in defending Suldanessellar. And the continuity issue I'm talking about is R.A. Salvatore's Drizzt novels that take place in the years after BG2 Throne of Bhaal before the Spellplague. None of them, not even the Hunter's Blades Trilogy give Drizzt time to leave Icewind Dale and return to Amn for any reason, although I've deduced that the game Demon Stone takes place a couple years before The Orc King novel.
Aerie has the most potential to appear in BG3 whether the custom character of the Bhaalspawn Saga canonically romanced her or not.
