Details about shipgirls are classified, and only Lt. Commanders and above have clearance.

However, their looks are not different from that of ordinary humans. Because of that, there are quite some objections about their treatment as mere weapons.

Still, their powers are formidable. After all they're humanoid warships, no less... Our only hope to fight Abyssals as of now are shipgirls.

It depends on the commander, but if someone who has the same thoughts as higher-ups sought to control the shipgirls... it's not hard to guess what kind of methods they'd use.

Treated like expendable pawns, becoming subjects of super-soldier programs mixed with human experiments, used as weapons of war... you of all people should know how that would be like.