If Hydrogen doesn't show up in Jack, then you need to check it's preferences. Go to File -> Preferences and click the "Audio" tab. The driver might be set to "Auto" or "Alsa" but you need to change it to "Jack" and then apply (it will give an error if Jack isn't already running). The "Connect to Default Output Pair" means that it will automatically connect Hydrogen's output to the system outputs in Jack... if you want to actually loop Hydrogen, then you need to connect Hydrogen's audio output to SooperLooper's inputs. Leave the "enable track outputs" unchecked, or it will make separate jack outputs for every single instrument in Hydrogen. (that option is really handy for multi-track recording, where you can eq, effect, and pan each drum voice separately)
If you want to run Hydrogen on its own and use SooperLooper beside it, you need to change SL's sync settings to "jack" and such... I think you need to change a few settings in Hydrogen too. It would be easier to come up with a good 4-bar drum loop and export it as a .wav file, and load that into SooperLooper.
Anyway, there's a few options. Let me know how changing the settings works for you. Good luck!