JRemote is mostly a remote control, but it has (at least) 3 fairly different modes of operation:
1. Remote control. This is the normal way of using JRemote, which just controls your MC server and tells it what to play and what zone to play it in. Anything that your MC server can play will be played. The sample rates, etc are all a matter of how the MC server is configured. JRemote is just a remote control in this case and does no processing, no conversion, nothing extra at all. It's just a remote.
2. Streaming media player. If you select "this device" in the zones section of JRemote, it switches from being a remote control to being a media player that plays audio and video on the JRemote device itself. In this case, the conversion of audio and video is handled by the JRemote app. There are probably some limitations on maximum sample rate as you have indicated. I don't know the various audio and video limitations, but I'm sure there are some.
3. Theater View remote. In this mode, JRemote's screen goes mostly black. It then allows you to swipe left, right, up, down, and click. By doing these gestures you can control Theater View on your HTPC. This essentially replaces the need to have an IR remote control with four arrows and a button to select. Since that's pretty much what you need to control navigation and selection in Theater View.
I hope that helps clear it up for you.
Brian.