Yes by default jackd stops pulseaudio, which desktop apps use. There’s a lot of obscure information online about how to get them to work together, but I think these days it’s as simple as installing the pulseaudio-module-jack package. I find this doesn’t always work, though.
Unrelatedly the exception in GraphDef_Recv: exceeded number of interconnect buffers. looks concerning, in the video I posted recently you can see how to start superdirt with more options. I think you might need to add this extra line to the list of configuration options there: s.options.numWireBufs = 128;