So how does one know how Touya and Yuki feel about each other, since they rarely say anything about it? The same way one knows that ANY two people share an emotional and physical attachment... body language, fingers touching longer than strictly necessary, long and wistfull looks, that sort of thing.
Of course, some of those things are more subtle than others: the way Touya tends to hover protectively over Yuki, fleeting glances that casual observers just won't catch. But of course, if you fall under the "obsessed fangirl" category (and I do), you catch every one of those. In fact, a large part of the fun of watching CCS might be precisely that. As for the more obvious things... well, these probably make you jump up and down while squealing in delight.
It's an interesting little fact that reserved, sober Touya gives himself away far more often than the open and friendly Yukito. Yuki might be grinning his typical grin, or be stuffing his face with a piece of pie that Sakura made for him... and in the background or off to the side, Touya is staring at him in a way that makes you wonder why the tv isn't catching fire. And it's not just that, of course. It's Touya's whole attitude toward the other boy, at once tender and fiercely possesive. Just watch him. He'll stare murder at Syaoran if he catches him blushing over Yukito, and might proceed to make a demanding, even petulant bid for Yuki's attention. It's like he's saying "he's mine, so back off". Interestingly enough, he doesn't seem to mind in the slightest when Sakura goes all ga-ga over Yukito.
As for Yukito, he's much more discreet, so much so that at first one might wonder if it isn't a one-sided infatuation on Touya's part. (Excuse me a sec while I go do penance for uttering such blatant blasphemy). Upon a second, more carefull look, however, it's quite obvious that Yukito returns Touya's feelings, by the way he not only readily accepts Touya's implied claims over him, but often ends up responding in kind to Touya's displays of affection. Like I said, I think Yuki's just shy, and also sort of an innocent at heart. Both of these things probably make it particularly difficult, if not impossible, for him to take the initiative.
Ultimately, the way they behave with each other is evidence to more than just chemestry or even romance; it hints at a a deep, pysical involvement. It's never openly stated, of course, but the way they touch just speaks of too much familiarity, too much surety in the other's response. In Touya's case, it speaks of desire and passion too fierce to be contained; in Yukito, of total surrender. In both their cases, it speaks of total trust and ultimately of love.
In other words, when Yukito spends the night at the Kinomoto's home, you can safely bet that they're certainly not going to spend the whole time studying. Pure lime.