How do you remove the weapon from a unit w/o changing the .nif?

Unit editing without editing the unit is impossible. One thing you can do is have multiple .nifs and change them via Python when you need to.

Well could it be done by editing a .dds file?

You could make it nothing but an alpha channel aka transparent, but then the unit would be swinging around invisible weapons.

Well if he can't fight he won't swing it.