The Seafile Admin Manual says either is acceptable:
The data files are all stored in the /data/haiwen directory, so just back up the whole directory. You can directly copy the whole directory to the backup destination, or you can use rsync to do incremental backup.
mind that - of course much depending on your concrete hardware setup and desired backup schedule - even rsync will be no suitable solution b/c comparing the directory trees alone takes a lot of time. time in which the server application must either be stopped, or the origin data changed while running resulting in inconsistent copies. i’ve seen this at an instance with a few TB of data and maybe around 100 users.
cow filesystems with snapshot capabilities, e.g. btrfs, are generally recommendable.