I was actually thinking about that at one point when I was looking through my manga collection for Zelda. My first thought was "why isn't Wind Waker brought over here yet. I know there was a 4Koma on it. Unfortunate that they didn't complete the game." My second thought was "Wait, how come they skipped right to Phantom Hourglass? Where is Twilight Princess? This game would be an awesome dark manga! They better be drawing it next..."
I think the odds of them making a Twilight Princess manga is low. I've noticed they tend to use the books that didn't have much storyline so they can add their own plot to it. Like Four Swords, the Oracle games, and ALttP.
That said, they've also done manga based on games that had richer stories, like OoT, so I'm sure TP would be great too.