This is speculation.
Point Number 1.
Shizuka was already past the point of no return. Which literally means she went past the point where she and Nagate would have enough fuel to return to Sidonia. This is a very real and very deadly result for all of the knights. Even so, Nagate went after her. In addition to him being a hero, his actions gained the respect of everyone, so they left to rescue him.
Point Number 2.
The guardians are supposed to guard, not leave the mother ship. By leaving to rescue them, they left Sidonia open to attack. Rescue cost resources, most obviously fuel. Rescue of people past the point of return opens up the risk to Sidonia even more because of the time the rescuers are away. The rescuers can get attacked themselves, and it takes time and resources to replace every knight. So yea, they were officially abandoned because the risk and cost outweighs promoting a new cadet.
EDIT: the number was because each squad has 4 members, so there were 64 squads present. I'm not sure if this answers your question because I'm not sure what's so strange about the number.
EDIT2: The significance of the number 256 according to @krazer:
That's the the smallest tactical unit in the Ancient Macedonian army, which was the 256 men syntagma/speira. Take note of the parallelism structure and organization between Sidonia, it's Garde, and ancient city states