Ever since the 1.1.1 update to fix the extra heavy weapon ammo issue, on any gear I equip that gives me extra heavy AND extra special, the extra special is gone. My Armamentarium used to be able to hold 24 sniper. Now it's only holding 16 - which is what my regular chest piece can hold. I think the heavy ammo fix broke the functionality of the dual-extra pieces.
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I have noticed that going to orbit and starting a new mission wearing extra heavy perk Armour ( Armamentarium, etc) that 6/7 rockets become 4, but i suppose that 4 is better than 0, I've not checked special ammo or Armour that give more primary