With the dagger it's a case of the dagger existing before the chem article was added, and alot of the other chem weapons if i recall correctly. It should be updated to reflect current status, i figure dioxine overlooked it.
#006 is a simplification of the actual mechanics. Each weapon has its own individual modifiers for additional effects. There are no "classes" in the rule set, just groups of weapons that dioxine happened to gave similar modifiers. The article describes that dioxine gave an additional armor damage modifier to pierce weapons above 60+, and plasma. Again older article that's not quite in line with current rule-set.
At some point, hopefully soon, Dioxine needs to do a bootypedia cleanup pass. There are several other inaccuracies floating around that will trip up newer player, but not effect a player that was around for the alterations.