The deleted scene in question is one where the freshly resurrected Superman walks through the halls of the Kryptonian ship. The black Superman suit is there in the halls for Superman to take if he chooses, but in the end, he opts to take the blue and red suit that he wore previously.
Fan Nick Albright asked director Zack Snyder about the thematic connection on Vero, framing it as a callback to the line from Man of Steel that says, "All these changes you're going through, one day you're going to think of them as a blessing. And when that day comes, you're going to have to make a choice: a choice of whether to stand proud in front of the human race or not." Superman choosing the blue and red is him choosing to stand proud.
Snyder responded to the question, saying "I think of course it's that (what you said) and that now in one sense he has been born twice once on Krypton once on Earth and it is this reality that he now is starkly aware of as he moves through the ship."
Taking a little hiatus from my Twitter break to freak out a little pic.twitter.com/01W4puRU5Q— Smalls (@nickalbright) February 25, 2018
The black Superman suit itself is an Easter egg reference to the original "Death of Superman" and "Return of Superman" storylines from the comics. In that story, Superman returned without his powers and wore the black Kryptonian suit until his powers were restored.
For now, this thematic scene connecting Snyder's three movies remains a special feature detached from the film itself. If fans have there way, a cut of Justice League with Snyder's original vision restored will eventually see release, though there's some debate over whether such a cut eve exists. If it was released, it could possibly restore the villain Darkseid to the film as well.
Justice League is now available on Digitial HD. The film comes to Blu-ray and DVD on March 13th. Other upcoming DC Extended Universe films include Aquaman on December 21st, Shazam on April 5, 2019, Wonder Woman 2 on November 1, 2019, Cyborg in 2020, and Green Lantern Corps in 2020.