Hi Akira, mine was not set to zero but continued on where it left off. That's pretty much consistent with what I have read online. I think Nikon might think it's the number of actuations by the camera, not the shutter, that matters. Or perhaps they simply can't reset it, which wouldn't surprise me! In any case, it's nice to have that mirror lock issue resolved and confidence that the camera is working as it should, I'm pretty happy about that.
Note: they did reset the file-naming convention to zero, but that's not the same thing as resetting the image count for Exif. I think from what I read, some folks have the file name set to zero, and some don't. On mine they did a re-set of all the settings, so that pushed it back to zero.