Perfect Dark/WMG

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.
 * It's probably just a codename anyway.
 * The computer-controlled simulant in co-op is apparently Violet Dark, Jo's sister. Yeah.

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.
 * She might also have thought it was a different Dr. Caroll. Caroll isn't exactly a rare surname.

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.
 * The Motion Sensor Bomb is the Proximity Mine from Goldeneye. The cloaking device wasn't in the original game.
 * In the JP and PAL versions, however, the Motion Sensor Bomb is the Proximity Mine from Perfect Dark. It is only in the NTSC version that it uses the Goldeneye design.

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.
 * Those are all real guns, though, and pretty common ones too. They just go by fancy made-up names in Goldeneye.