They might be coming BACK to 5km eggs, but most of the ones I've gotten have been hatched from 5km eggs prior to Gen 3 being released. (I haven't gotten one in an egg since Gen 3 was released, actually)
I'd like to have them back in the eggs, actually; I've hatched more than enough Treeko and Mudkip in the past 3 months. So many that I don't need to worry about getting any candy on their Community day; I've got 500+ of each, mostly from 5km egg hatches.