I've stopped caring about perpetually redoing the combat deployment missions.
Silenced Rail GunAnti-Tank Rifle(bolt action edition), if you hit certain points will critically wound them. Otherwise, it takes 2 shots. (Or I'm just usually murdering everyone with less then B rank combat rating. The survivors are maybe high combat boasters. I should remember to take note.)
Headshots? I don't need no headshots, I got rail gun... or I guess when your squishy face is looking at me with surprise... that is a face shot.
Otherwise, there are other ways to deal with riot gears non-lethal. Good ol CQC and/or dog stun. They also go down from the stun shotgun in a few hits... I typically use the silenced one though, so at least 3 hits?
Oh right, how the intercept supplies stuff works... I think they are supposed to last 3 missions and/or 3 side-ops or something along those lines. It is really annoying when you can fire off 3 side-ops in 15 minutes, then wait +30 some minutes to remove 25% helmets or something like that again.
From my observation though:
Helmets, gas masks, body armor and flashlights, doing the combat deployment shaves off 20-50% of the chance for soldiers to wear those. (Minus event/side-op related guys.)
Weapons though is far more noticeable, except event/side-op related guys. I venture to guess that it isn't 100%, more like 80-99% reduction of the weapon type.
EDIT: Clarification