I will bet you one copy of Wizardry IX that your ninja, with any weapon, will get the secondary attack once you move him to the front 3. there's a front 3, and back 3, the back can only attack, and be attacked by Extended Range weapons (or thrown, or long range). unless hiding and surprise/backstab attack. in which case the secondary weapon has to be an extended range weapon (of which none exist, sadly), a thrown weapon (feather darts, shurikens), or a long range weapon (Cobaltine Power Glove or Mystery Ray)
and if your going that route, get an Extended Range weapon, like the Cat O' 9 tail (like you have much choice for one), so your ninja doesn't have to waste a round hiding, and also you don't have to worry about criticals spoiling the hiding, and forcing you to hide again. another thing is, that the character is targetable, and will be targetted more often, and with his low AC, won't be hit, saving another character the pain.
btw, AC is important, and you get this via Level, Speed, and most importantly, Ninjutsu. more often you hide, better ninjutsu you get a lower AC. equip the ninja with a staff or Annointed flail only, and have him hide/fight repeatedly against savant guards. a few protective spells couldn't hurt his survival.