Are arrows the only projectile weapon that can pierce through armored helmets?

No! You can use .50 caliber sniper rifles equipped with armor piercing ammunition to kill the Eden's Gate Heavy Gunner with one shot through the visor.

Armor piercing ammunition can be purchased or found throughout Hope county and is used via the radial item wheel. AP rounds can be applied to most weapons but the few heavy snipers are the only weapons that can kill the armored enemies in one shot while using AP bullets. While it isn't a one-hit-kill, any firearm firing the AP bullets will make short work of a heavy gunner.

From what I can research, shotguns can also kill the heavy units with one shell but I don't feel comfortable sneaking that close to one to test it myself. I prefer long distance relationships over close combat engagements.