Well I think with Days of Future Past movie she was brought back to life. Apocalypse and Logan were alternate universe movies if I understand correctly.
Yes. Time was changed in DoFP, so now Jean's alive again. This story is set after Apocalypse, but before Logan (obviously).
As for the original question, I've heard nothing concrete, but rumours indicate there will be aliens, but not necessarily the Shi'ar as we know them. Jessica Chastain's rumoured to play the lead alien role. However, she's also said to be a shapeshifter. The name of the role hasn't been revealed. It's also been said the script is more in-line with Claremont/Byrne's original story.
I suspect Daniel Cudmore and Lamar Johnson might play aliens, as well. Although Cudmore has played Colossus, they strangely haven't said that's who he's playing for this. Maybe one of the Imperial Guard?