BackupPC uses hardlinks to pool files common to different backups. Therefore BackupPC's data store (__TOPDIR__) must point to a single file system that supports hardlinks. You cannot split this file system with multiple mount points or using symbolic links to point a sub-directory to a different file system (it is ok to use a single symbolic link at the top-level directory (__TOPDIR__) to point the entire data store somewhere else). You can of course use any kind of RAID system or logical volume manager that combines the capacity of multiple disks into a single, larger, file system. Such approaches have the advantage that the file system can be expanded without having to copy it.
Any standard linux or unix file system supports hardlinks. NFS mounted file systems work too (provided the underlying file system supports hardlinks). But windows based FAT and NTFS file systems will not work.
Starting with BackupPC 3.1.0, run-time checks are done at startup and at the start of each backup to ensure that the file system can support hardlinks, since this is a common area of configuration problems.