Because the general mode a spear is used in, the thrust, it has the potential to be better against armor. If you get a good, clean, perpendicular hit against the plane of the armor.
Arrows, the same.
A sword in a thrust could have the same advantages, because they are not only used to cut.
The problem is, that most weapons in these categories are not (traditionally) designed to do this. If you look at most spears, arrow heads, and sword points, they are broad blades. Broad blades are not good at penetration against rigid items. They can penetrate, but the design of the head is not actually designed for that.
There are some spears, arrows, and swords with specialty points that are designed for armor penetration, but certainly not the majority.
So giving all spears (or any other weapon) a cart blanche +1 to all damage because its good against armor, feels a bit... off.
And back to my shortsword reference. My question actually was (should have been?), if a shortsword is NOT used in a thrust capacity (or if a Hewing Spear is NOT used in a thrust capacity), are you still giving it a +1 in your system?
SDLeary