Reputation items had both since 6.2. Archeology I don't think so, but then again archeology has always looked like they came in batches. They'd always proc on all my 12 chars at the exact same time. Either they're on a cycle or blizz has a button they need to press to make them pop for everyone at once.
I don't know what is going on with archeology ... maybe you only get one of those missions every three months if you don't do archeology on a regular basis.
Rep items ... I don't think I have had any since 6.2 except I got a medallion of the legion from a rare 675 mission.
arch missions have always been super rare; my main has had maxed arch since like week two of WoD and has logged in pretty much daily, and I've still only seen about half of them
since the rep token missions also reward gold, the 6.2 changes might have resulted in fewer of them if you have a large number of alts. I don't think we really know yet how all that stuff is accounted for though.