Joanna and Jonathan got married and Jonathan took Joanna's name.Perfect Dark Zero takes place in 2020, and Jonathan's last name is listed as Steinberg, with "Dark" being Joanna's family name. In Perfect Dark, which takes place 3 years later in 2023, Jonathan's last name is Dark. They married during those 3 years and Jonathan took her name...probably because it was much cooler than Steinberg.
Joanna simply completely forgot about the name Dr. Caroll between Zero and Dark.3 years is a long time to try and remember a mostly unremarkable (never mind his accomplishments) somewhat elderly scientist who died during a rescue attempt amidst other scientists who may have died during said rescue attempt. And when Joanna finds out that the Dr. Caroll being held hostage by dataDyne is a floating AI programmed with the personality of that long-dead scientist, and considering the AI is working on roughly the same project the original Dr. Caroll was working on? Gee, hard to believe she doesn't connect the dots.
Joanna Dark was intended as character in SSBM.Evidence is with motion sensor bomb and the cloaking device. I guess when Rare being bought by Microsoft it couldn't be done.
Perfect Dark and the original Goldeneye are set in the same universe.This would explain the guns in the glass cabinets in the firing range.