To use your Harmony (or any universal) with the Hopper, enable IR mode in the Remote Manager on the Hopper. It should also work with your Joeys, but all should use address 1 now. Joey is supposed to have an IR receiver which sends commands to the main Hopper via MOCA. The nice thing about Hopper is IR and RF work simultaneously, so you can use universal IR remotes and the UHF Dish remotes at the same time. My IR universal remote is working fine with Hopper using the same Dish codes as the VIP 922, address 1.
No universal remote will work directly with Dish RF. The Hopper remote model 40.0 uses a new advanced 2-way RF system called ZigBee which is essentially an RF remote PAN with pairing, discovery and encryption like Bluetooth. I wouldn't expect that to be integrated into any universal remotes anytime soon.