Since you squad never runs out of ammo, it seems to me like a no-brainer to pick the headshot damage over extra ammo capacity every time for your squad. Or am I misunderstanding the wording, and the bonus actually increases clip capacity instead of spare rounds capacity?
It's spare round capacity.
BUT, This additional capacity transfers over to Shepard when Squad Ammo powers are used.
This is arguably worthwhile, since, at least in my experience, my squadmates are lousy at taking headshots, and as a Vanguard, I rarely bothered.