She loves him, she's just very independent :)

Yuuki and Kaname are romantically invested in each other; it's just that Kaname is not possessive and let's her roam around freely. Yuuki, still young, would not as much think about how she feels for Kaname although she did admit she loves him. Besides, in VK, she has those issues with her past she has to deal with. So by VKG, when she turned into a vampire, she was more self-aware and certain about her feelings with Kaname.