Going into this game I was not expecting it to be a love story. Probably due to 9S design but at the beginning I was like "they better not ship 9S and 2B" and then by the end " I was crying for them to be together".
Same for me.
Up until final 2E unveil, 2B/9S interactions were vague enough to not make any final conclusions and events were happening super fast that it seemed like it didn't matter how they really felt.
But retrospectively it all makes sense now considering their situation and what they knew about it. And ending E couldn't be more justified for them.