I was aware Gosalyn was going to be in that episode. Honestly, I think it makes sense that they waited to introduce her. I would assume that her parents are dead, hence why she was living with her grandfather. Lena could still be involved in a DuckTales connected Darkwing Duck reboot, but I doubt it will be in the way you suggest.
With the way things played out, I kind of expect that Morgana is a fictional character in the DuckTales 2017 dimension like the Fearsome Four. Drake and Launchpad mentioned that the Jim Starling series had a “Just Us Justice Ducks” episode. I’m guessing that in this version of the story, the Justice Ducks consisted of Darkwing Duck, Neptunia, Stegmutt, and Morgana. Obviously there would be no Launchpad, Gosalyn, or Gizmoduck, just as there would be no Negaduck on the villains’ side.
That being the case, I expect that Morgana won’t be in the Darkwing reboot if it’s a DuckTales spin-off, except under certain circumstances:
If Drake ends up traveling to the universe of the Jim Starling Darkwing Duck series as he searched for Gosalyn’s grandfather in other worlds.
If a portal to that universe opens up in St. Canard again.
If the actress who played Morgana somehow gains real magical powers and decides to emulate her character, either as a hero or criminal.
Some fan of the show who liked Morgana gains magical powers and decides to take up the role.
I suppose there’s also a slight chance that Morgana could be real in the DuckTales 2017 world like Steelbeak, Gosalyn, her grandfather, and Taurus Bulba. The Justice Ducks connection makes it seem unlikely to me though.