I have never had emus, so my concern may be unwarranted...... But, they appear to be scabs caused by pressure on the hocks. (I would concerned about staph entering under the scab)
I may be wrong about this, perhaps some one can chime in and let us know.
I think being on a nice thick soft bedding would be of benefit. I am wondering if the sores/callouses on his hocks are caused by the hard floor in the crate.