Because its Nojiko Miyazaki now, while Nika is still Nika Cyrus. Its not a matter of incest patch or not (the incest patch just isnt up to date as is shown in a lot of renders). There should be no (incest)-name-fakeing nessecary as Noji isnt a LI and adopted them.
Which is strange, there has to be a reason for them having different surnames. Ocean didnt just thought "Oh let me just change Nojiko's surname into something else for no reason". We just dont know why.
Youre right that Noji adopted the blood-siblings Nika and Nami at a very young age, yet the have different surnames.