Agreed, Archivematica and the Storage Service are not FHS compliant.  Archivematica puts the shared Directory structure used in processing in /var/archivematica, and the storage service followed this convention by putting its internal data in /var/archivematica/storage-service.

Both should probably be in /var/lib/, not /var.  It seems to be okay according to both FHS and debian/ubuntu practice for a package to delete items from its own /var/lib/<package-name> directory.