Nova Prime’s absence in Guardians of the Galaxy Vol. 2 is understandable given that the Nova Corps played no role in the story.
As for how Nova Prime might have cameoed in Guardians of the Galaxy Vol. 2, I suspect we would have seen her back on Xandar reacting to one of Ego’s seedlings expanding and consuming the planet.
Gamora and the other Guardians had intended to bring Nebula back to Xandar so that the Nova Corps could put her on trial, but they were attacked by the Sovereign soon after and didn’t make it to their destination.
Nebula and Gamora patched up their relationship by the end of the sequel, but that doesn’t change the fact that there’s still a bounty on Nebula’s head, so she’ll need to be careful not to be caught by someone else and dragged back to the Nova Corps.