Yeah, I guess Wind Waker did hit it, at least in Japan. As you said, though, that probably wasn't a good thing.
Didn't Miyamoto upend-the-tea-table once one of the artists showed the team a drawing of Toon Link? Being on time is relative at that point. Even if we don't count the setback of changing the art direction, Nintendo still ended up cutting two dungeons from The Wind Waker to prevent a delay.
That said, unless we're counting Four Sword Adventures, I'd still give it to Majora's Mask which, as you said, was designed for a quick turnaround. This was after Ocarina of Time was a delayed a bunch of times. If we want to count handheld Zelda titles, I haven't read about any issues with A Link Between Worlds though it should be noted that the game borrows much from A Link to the Past. Before that, Spirit Tracks carries the same distinction as Majora's Mask (in that it used the previous game's engine for a quicker development cycle). Phantom Hourglass was originally meant to be a Four Swords game. Hyrule Warriors, Four Sword Anniversary, The Minish Cap, and the Oracle games weren't developed by Nintendo. Link's Crossbow Training is a few mini-games, and it uses Twilight Princess' engine and assets.
Most Nintendo-developed Zelda games not specifically meant to take advantage of existing assets have been delayed, if not restarted entirely. This isn't a bad thing as I'd personally rather every developer delay a game before releasing one that isn't good. All things considered, I would be rather surprised if Zelda Wii U releases without any major development snags, especially since Nintendo is trying something it has never done ever, Zelda or otherwise.