Kingdom Hearts series director Tetsuya Nomura talked with the Game Informer staff about Kingdom Hearts III. Specifically, they had asked him about the inclusion of the Gummi Ship in the game. He says it'll be in the game but he cannot yet reveal how it is or what's become of it.
You can check out the full quote below:
"In terms of the Gummi Ship making its return, I can confirm on that, but how it is or what has become of it, we’re not able to reveal it at this point.
We ask you to stay tuned for more information."
Nomura also expressed that the Kingdom Hearts team tries to pay attention to what's received well by fans and that they always want to try something new and always try to tweak old mechanics for Kingdom Hearts III. You can check out the full quote for this below:
"The staff members on our development team always want to try something new, so even with previously introduced mechanics, they always try to make it their own or tweak it. Even if it is small or minor, we customize it so that it’s for Kingdom Hearts III."
UPDATE: During an interview with IGN, Tetsuya Nomura reiterated what he stated in this Game Informer interview about the Gummi Ship in Kingdom Hearts III. View the full quote below:
"We can confirm that we do have Gummi Ships in Kingdom Hearts III because it is a numbered Kingdom Hearts title. You can expect that to show up, but it has evolved. We can't say how it has evolved, it's a secret, but Gummi Ships will be in Kingdom Hearts III."