alot of speculation over this topic, but my personal theory is that samantha is nikolia's daughter, after black ops 2 first came out, me and friends where going through the classic maps for black ops 1 we kinda peiced it together,
here is how the thought process kinda went as i cant remember exactly but i do remember some key elements of how we came to this idea,
so we played through the first 3 classic maps and nikolai quotes suggest he was starting to regain his memory (just humour me, forget what you think you know just for a sec)
then we played die reise (4th classic map)
and nikolai starting saying things about his abandoned daughter and how he beats his wife and kills em and all other sorts of stuff, then later on we realise maxis and richtofen captured the 3 characters and did a bunch of tests on em, then we went through and listened to all the radios which confirmned that fact.
so who's to say nikolai isnt sams father and when maxis and richtofen where doing the tests that maxis didnt take sam and decide to raise her as his own?? hence why she thinks he is her father??
just my theory in a nutshell so i dont bore you guys with my nonsense + (false information if im wrong)