Woah, I never really thought of that. I'm kind of sad now.
I mean, honestly, I assumed Agatha either retired or passed away. That makes sense, but Lorelei just kind of disappeared for no reason. It was mentioned in FR/LG that she had strong ties to her home town in the Sevii Islands, but I never thought about what effect the Cinnabar eruption would have there tying to this. Even if she's not dead, maybe she abdicated her position to focus on more humanitarian efforts for the Sevii Islands.
With the extreme paucity of appearances and references for either character past FRLG, it's hard not to come to a grim conclusion about Lorelei and Agatha. :( Since it's very unlikely that we'll ever see or hear from them again in canon (outside of, maybe, another Gen 1 remake), all we can do is speculate. As it is, they're pretty much just as retconned out as the likes of Jessie/James, Kris, and Green.
Now as to why GF got rid of them in GSC in the first place... Well, that question hasn't really been answered, either.
Obviously, they wanted to change up the E4 in GSC to show the passage of time and mix things up for people who had previously played RBY. And, since he was the leader of the group, it made sense to have Lance return and play a larger, more fleshed-out role.
But, why keep Bruno over Lorelei and Agatha? Why drop the women in favor of the other man?
As far as Agatha goes, it's fairly obvious: Morty. GSC introduced a new Ghost specialist, and due to the extreme paucity of Ghost types, he had to have the same ace as Agatha (Gengar). Agatha was way too redundant with Morty, and that, combined with her old age, made it easy to get rid of her. People could just assume that she either retired or died and move on, simple as that.
But, Lorelei? She was too young to either retire or die. And, she wasn't really redundant with Pryce in the same way that Agatha was with Morty (their teams had nothing in common except Dewgong, which was easily replaceable on Lorelei's team). Why keep Bruno over her?
Time to grab your tinfoil hats, because I have a far-out theory: CENSORSHIP!
While Lorelei's ace in the games is "technically" Lapras, we ALL know which Pokémon is REALLY most associated with her. It's the one she's been constantly depicted with in other media, including her (somewhat infamous) anime appearance, enough to where it's literally impossible to separate or disassociate her from the Pokémon. Jynx is to Lorelei what Dragonite is to Lance or Pikachu is to Ash. In other words, giving the spotlight to Lorelei inevitably means giving the spotlight to the Blackface Pokémon. There's no way around it.
Combine that with the
borderline softcore pornographic appearance she made on the anime, and you have a character who is (through no fault of her own) associated with a lot of unsavory, family-unfriendly things. When you consider
how much got censored out of GS for these exact same reasons, it's not a stretch to think that, maybe, GF wanted to avoid any further controversy by cutting Lorelei out.
Sure, Will had a Jynx, too, but it wasn't his highest-leveled Pokémon, nor was the Pokémon super closely tied to him. It's easy to forget that Will even had a Jynx on his team, so thinking of him doesn't make you automatically think of the Blackface Pokémon. Him being an asexual, fully-dressed young man and not a beautiful young woman in a miniskirt certainly helped his case, too.