Lucrecia meant to sleep with Vincent rather than Hojo on the night Sephiroth was conceived, she got drunk that night and accidently thought Hojo in the dark was Vincent, Hojo of course decided not to tell her and the reason Hojo REALLY shot Vincent was because Lucrecia was screaming his name instead of Hojo's that night
On a more serious note, Cissnei is still alive but defected from the Turks and Shinra after Zack's death and instead went to live a quiet life somewhere away from anything to do with the company. She also felt guilty about being unable to stop Zack's death and as a result felt unable to go back to Gongaga and deliver the news to Zack's parents about their son's fate.
Aerith's fear of the sky comes from her being raised in a building and then under the plate for so long. The sky is so natural, wide, open and free; something Aerith could never fully comprehend after her years in captivity and being under constant surveilance from Shinra, this fear dissipates once she leaves Midgar and sees the open world for the first time with Cloud and the others.