The new Dish Network Hopper H3 only seems to support mkv for direct play. I think it will also be this way on the Hopper With Sling once it gets the new Carbon UI. I have created a new profile that is working and plays all videos. Most of my movies were mp4 and are now transcoded but at least they are playing. Also, the new identifier/User-Agent is ZiP. Not sure if there is anything that can be tweaked, but thought I'd share to at least get it started.
EDIT:
Since the Hopper 3 was updated to version 308, the standard Dish Hopper profile works with adding the User-Agent:ZiP You should be able to add this to the system profile so we do not need a custom one anymore. I have left the other profile, Dish Hopper_HWS_CUI.xml for those that are still on the Hopper W/Sling and Carbon UI. Dish has not been updated yet and will still need the custom profile.
Dish Hopper_HWS_CUI.xml
Dish Hopper3-4k-Joey_308.xml