I don’t know of any adjustments to make to seafile that can improve the performance of the seaf-fuse. The performance of fuse can sometimes be improved with new kernels, but sometimes you also see regressions. Generally fuse doesn’t give great performance ever, but it can be “ok”. I worked for a company whose product relied heavily on fuse, and their filesystem was also pretty slow to index lots of files.
I suspect (but don’t really know) that performance would be better with mysql than with sqlite.
You probably have seen the official backup guidance, but if you haven’t, look here. It does mean doing the backups in a very different way, so might not work for you (which is probably why you are doing what you are doing), but worth mentioning.