Arjen,
I will pass on your recommendation that we place our start up daemons for the BIM Server in the Library/LaunchDaemons folder.
As you correctly identified the issue, the BIM Server is coming on line sooner than the RAID disks. As a result it is not finding its databases. I can empathize with you. It certainly wasn't a very pleasant state, and you were probably concerned about your data. Fortunately, after this happens, if you stop the BIM Server application and restart it, it should find the database files without any data loss.
For the time being I would disable the "Start BIM Server with Operating System." This will prevent a similar issue when your system re-boots.
I am sorry for the inconvenience.
Graphisoft Technical Support