I did a full-upgrade and the server doesn't boot anymore with 4.9.0-8-amd64. This was tried several times.
While this could be a hardware issue, it does boot with 4.9.0-7-amd64, having a low, but possible reason to be a kernel/OS regression.
Loading freezes at:
Loading ramdisk... step
I will leave the server with 4.9.0-7-amd64 for now, as I cannot leave it depooled for long.