It's been a while since I've last seen this series, so forgive me if I make any mistakes.
It may have been implied earlier on in the series that Hinata had a crush on Yuri, given his overprotectiveness of her, how flirty he acted with her at times (though perhaps that's just how he acted in general), and how dedicated and loyal to her he was; things did change slightly once Yui came into the picture.
Yui, much like Yuri, would eagerly abuse Hinata (poor guy can't catch a break), though she did so with wrestling holds, but he would begin to retaliate and the two got along well. The two would banter and have their spats just as very close friends or siblings, or perhaps even couples, would.
Minor plot spoilers ahead.
Anyway, most importantly, he tells Otonashi at the
graduation (before he moves on) that he thinks he's saved
up a lot of luck, and that he'll use it all to meet with Yui. I
think that alone is enough to prove his feelings for her.
I sincerely doubt that, though he is kind and selfless, he would have the heart to lie to Yui's face about the one insecurity and dream that must have plagued her mind and heart since she first really took in what being paralyzed as she was meant.
As for earlier hints, well, I think it's just something you'll notice here and there while rewatching, as things happen that just make you think "Oh, he totally likes her."
