I bet the author glanced at their site named "Zelda 64" and assumed that's how they referred to OOT not realizing they have other projects (some not even on the N64 now) as well.
Ah I didn't notice the source website. That makes a little more sense (on the reporting side at least). I wonder if the fan site is named that way to avoid trademark issues with the full name?
It might be to evoke nostalgia for when it was still in development and the press was hyping it up under that name. Even Nintendo used it occasionally (including for a preview feature in Nintendo Power).
zelda64.com was also the official website when Ocarina of Time came out, presumably because, at the time, the zelda.com domain was already taken by a porn site. That was an interesting discovery for 10-year-old me.
There are teams working on both the OoT decomp and a MM decomp, so I think that combining both of those under the Zelda64 heading is neat--especially with the callback to the pre-release OoT name.
Of course, then another team started a Minish Cap project, and now the name is a bit out there.