I see merit in the memory wipe theory (Ginny doesnt have a DF, same appetite, Bonney doesnt have any Buccaneer traits), if something bad happened to her and Kuma wiped her memory to erase the pain, then it could be one of the saddest things to come from this series.
However, there are things that rule this out tbh:
- Bonney has seen Kuma's memories, and she still refers to him as father, not as her old self.
- Bonney doesnt resemble Ginny when she is young (different eyebrows, no freckles, etc)
- Her alternative future move against VP almost sounds like a future where she "would" have had Buccaneer blood but didnt
Honestly, my theory is that she is either Ginny's daughter (somehow) or made into a clone by VP (when she is captured, then Bonney is spared in an agreement that forces him to be a Shichibukai), but is not actually Kuma's daughter.
The former option has real fucked up implications, so Im willing to bet she was captured and cloned, and the fact that she was at Egghead as a child supports it. At this point VP would have created Stussy so she would definitely been a successful clone.