Nath's arms were removed after Sora's defection from the military. To prevent others from doing the same, they modified Nath and removed her arms, hooking her up to many more machines, to prevent her from ever have the freedom that led to Sora's defection.
Nath's Hyper, Another Ultimate Weapon, is a reference that Nath is the attempted replacement of Sora, who was considered the "Ultimate Weapon" and thus she is "Another Ultimate Weapon".
Nath is named after the Beta Tauri star in the constellation Taurus. This star is also known as Elnath, which in Arabic, translates to "the butting".