The reason that so many sailors died was because of the secrecy of her mission. Only a handful of very high ranking officials knew where she had been and where she was going afterwards, so there was no one to worry when the Indianapolis didn't arrive in time.

Because of this tragedy, the Navy instituted a new policy that made it impossible to ever again "lose" a ship. Ships, to this day, are required to send to their commanders detailed sailing routes that include not only the route but also the speed and times for departure and arrival. This information, all together, is known as a PIM, or plan of intended movement, that can only be deviated from with a message to the ship's commanders.

(The messages are called MOVEREPS, aka Movement Reports.) The Navy has an acronym for everything.