Yep, Caps, Masks, and Helms are all (S)haped items. This means they can't be worn in conjunction with each other.
Masks have a coverage of 50 and no armor level, even when made of metal, and can not be made by dwarves, unless you mod the game, resulting in very poorly crafted pieces for your use.
A metal cap has a coverage of 50, but has an armor level of 1 when made of metal, can be crafted natively.
And Helms have a coverage of 100 and an armor level of 1, 2 when made out of metal.
What does all this mean? Helms are the bee's knees without modding. The simple thing to do would just be to remove the [SHAPED] tag from the masks.
But, If you really like masks then the thing to do would be to go into your ENTITY_DEFAULT.txt file and add [HELM:ITEM_HELM_MASK:FORCED] somewhere under the ENTITY_MOUNTAIN, right under the helms is where I put mine. They'll be made by your armorsmiths, clothiers, and leatherworkers. Since they don't have any armor levels at all they'll be claimed by your civs. If that's a problem you'll need to add either [ARMORLEVEL:1], you could also use [METAL_ARMOR_LEVELS] if you want the metals masks to be better than the leather and cloth ones, or even just metal armor levels.
I know the changes to the entity file will require a new gen if I'm not mistaken. Probably also for removing the shaped tag.