Navy intelligence was concerned that ships could be sabotaged and ship movement and/or cargo information would get out. The mob/union owned the docks at the time. Luciano was in prison serving around 40 years so his interest in the deal was that the Federal Government agreed to move him from a prison away from NYC to one that was close by so that business associates, family, and friends, could visit him.
Of course letting Americans know that they were working with the mob wasn't something that they wanted out thus why you and I didn't read about it all those years ago.