As others have said, the 52 and the 40 remotes are RF only to the Hopper. These remotes output IR ONLY for other devices (TV, Aux, DVD). You'd need to go back to something like the 21 remote to be able to output IR for the Dish receivers.
Also as others have said, Hopper 3 will respond to IR commands used by virtually all other Dish receivers.
There are only a couple of issues that I ran across:
The OPTION button on the 52 is essentially the RED button on previous remotes. The other color buttons work also so you may or may not want to abandon them.
Good luck.