I think you go much too far with interpretation. IMO there is no reason to think that relation between Yen and Ciri is different then in books. This relation is just not shown in the game. Mainly because we play Geralt and it is a game, not a book.
I agree that there could be more Yen Ciri interaction, but there are many things that could be added. Like Yen Triss quarrel, more romance scenes for Geralt with his chosen love, more changes in interactions with Triss and Yen (like, when you say Yen that you do not love her, then she do not kiss you at KM, while Triss do that) and so on, But all this makes game production longer, more expensive and more complicated. You need more dialogs, more cutscences, more coding and more voices made in many languages.