Picking up on romantic hints in previous Zelda games may have been difficult, but I don't see how somebody can not pick up on the romantic hints between Link and Ilia. Shipper or not, it's plain as day. You don't need blatant "I love you" dialogue to get the point across. There are plenty of slow-motion scenes between the two, and a huge focus on saving Ilia (and the rest of the kids). Before Link and Midna bonded, Midna did point out noticeable affection between Link and Ilia.
Another huge finger-point at the relationship between the two is the scene where Ilia remembers. Once she comes to, the children all run off to give her and Link some private alone time. Classic, as scenes like that have been used in romantic scenes for ages. Ilia even tells Link she'll wait for him. Oh, and they have yet another slow-motion scene there. Cheeeeesy!
Now, yes, they are best friends that is certain. I think a puppy-love (I say puppy-love because they seem to innocent at the beginning to be OMGINLOVE!) relationship between the two was very present in the earlier parts of the game. I think it's obvious that Ilia has feelings for Link for the duration of the game. I think Link felt the same for her in the beginning, but something tells me his quest matured him... he seemed to grow a bond with Midna, but eh, that is debatable. In any case, by the end of the game, Link seems to fall out of whatever interests he had for Ilia. He seems to be more involved in what else is out there. This is probably why he leaves at the end.
Still, I think that romantic interest was very important in TP because of Link's age. In games where we play a child Link, it's not so important, but as a person grows and matures, they develop more interests like relationships.
HOWEVER, it's not made to be an underlined point. This is a game on adventure, not romance. It's not Final Fantasy where a relationship is core to the story. A romantic interest helps emphasize Link's closeness to adulthood, but it's not the focus.
Ilia may or may not be a suitable interest for Link, but that's not the point. Her feelings for him were easy to pick up. That doesn't necessarily make her his love, though, it just makes her a romantic interest.