So weirdly enough, I upgraded esxi to 6.7, completely reconfigured the network with seperate vmkernels and port groups, and now the dual 40gbe cards are humming along perfectly.
I think it might have been a combination VMware issue with their new html5 ui (because frankly the thing is full of very strange bugs all over the shop) and my own incompetence.
Passthrough on the other hand still doesn't work at all, with the same error message about IRQs.
I guess for my purposes this might work better since at least now the physical 40gbe links are also available to other VMs, not just Freenas.
Thanks everyone for taking the time to help!