Saavik, even after being told about the protomatter, declared she had no knowledge of the Genesis torpedo Kruge wanted. Since Vulcans don't lie, that was it.
That would have been after Saavik learned from Spock that Vulcans do lie, though. So it's probably a deadpan lie.
The rest of it was in the computer Khan stole and was destroyed.
Would this really be realistic, though? The team was
in contact with the rest of the universe - it could even commandeer the services of a big starship. Why shouldn't they be sending at least monthly reports on their progress to their superiors? Of the "here's how Genesis looks today, component by component, line by line" sort, rather than the "here's how we're keeping our schedule" sort, that is.
Just because Spock and McCoy don't know about it doesn't mean a thousand others in and out Starfleet wouldn't, too.