Is ist an error that the Arquebus in the Enemies within Supplement) lacks the "Primitive"-Special rule, or should this archaic piece of junk equipment be strangely effective against modern armours?

Well Primitive in DH2e is a lot less brutal than it was in the first edition. The lack of the quality is functionally about the same as just not having as high a base bonus damage.

Its definitely a somewhat effective weapon, given its damage, rarity, and other special qualities