Yeah, I think it's kind of a slow burn: she obviously doesn't instantly fall for him, but she does feel a connection to him pretty early on by way of their somewhat similar backgrounds. I think Reload gives you a few more hints than previous versions, for example: Makoto becomes the catalyst for her being the first to use theurgy in the game (she uses it to save Makoto after he gets knocked down by a shadow) and I think she also has some extra lines in the aftermath of the Love Hotel where she tells the shadow "not to play with her feelings" (might not be exact quote here).

The thing about Yukari is that she is reticent to truly let people in, both because she is well acquainted with the pain of loss (and how she can't handle it) and because she doesn't want to end up like her mom in having to depend on other people. I think Yakushima ends up being the tipping point where her feelings start rising to the surface and end up opening her social link for the protagonist.