Obsolete Material
Yes.
They can be exchanged for reputation with one of the tower factions (New Monarchy, Dead Orbit, or Future War Cult), or exchanged at a 1:1 ratio for new armor materials in the tower. All armor (new and old) has been switched over to the new singular currency, so there are no drawbacks to switching them over.
Yes they should be AFAIK
A quick peek through my vault at older Year 1 armour that I never fully upgraded but don't want to dismantle shows that the remaining upgrade slots now want Armor Material instead of the class-specific armour materials.