Hello everyone,
I hope this is the right place to share my experience with a similar problem. Cause I've been troubleshooting quite long and hope people can profit from my solution. If that's not the right place to post such a thing feel free to correct me.
My Problem
After I upgraded my TrueNAS from Version 12 to 13 I had troubles starting it again with wake on lan.
Solution
Had to do a fresh install of TrueNAS 12. I assume, that the TrueNAS 13 (or FreeBSD?) had troubles with the driver of my NIC. (I'm using an old Realtek NIC) and I think that's why TrueNAS wouldn't start with this new version.
Doing that I learned, that I can't import a configuration backup from a newer version. So I had to reconfigure my NAS. In the future I will always save a configuration backup of my NAS before upgrading it - if I ever upgrade it.