I saw several wagons last week when we were there, but only in Downtown Disney area, not in the parks.
I actually saw one family pulling their wagon (and triplets) back towards the GCH at about 10am one morning when the park was due to open. Looks like they had been turned away at the bag check. They were going into the walkway between DTD and GCH (near Libby Lu). The father did not look happy.
HTH
Angela