I know that Kusanagi Motoko is often nude as part of her
camouflage during the anime. And in that context, it's expected.

But...

...isn't Kusanagi (or, her cyborg body, at least) fully naked
except for the headset over her eyes and transparent veil
across her face?

(Update: yes, "thermoptic camouflage" -- but also fully transparent
themoptic camouflage. Also, other characters wear clothes
while using thermoptics, so was there ever an explanation of
why Kusanagi need to be naked?)

The whole "naked assassin" idea is obviously done in order to
show a sexy woman handling weapons, so it seems kind of silly
to tease the viewer with ScarJo wearing a beige onesie
instead of trusting us not to have a heart attack
at the sight of her bare nipples...

...or maybe they could have just given her clothes.

That could be what seemed strange. I don't know.
Did you have that "huh?" reaction, too?