Ok, so you have nice natural boundaries between systems. If you're dealing with something processor-like, you have really good chokepoints where for example ALU / register / caches connect. The task may be way easier if you deal with one of them at a time. Maybe even abstract anything less interesting (memory/cache?) Would visualising things per-system work better for you, or maybe visualising separate systems getting affected instead of specific nodes?

Having the structure of the device available should also help with the layout - we know you can group the nodes logically into independent boxes instead of trying to auto-layout everything.