I experienced an issue very similar to that described here - the Zyn synth LV2 plugin failing to open a GUI and then crashing to desktop, in Ardour on Linux. But the fix that worked for me was straightforward, once I eventually found it
Somehow my Zyn install (can’t remember how first installed but probably updated to zynfusion via the kx repos) was missing a crucial package: zynaddsubfx-data. once I sudo apt-get installed that and restarted ardour everything was good.