You may want to read Uploader unsuitable for folders of numerous small files
I complained about TCP/round-trip (and Pydio processing overhead) incurred by every file causing the web UI to be unable to handle efficiently a situation of 3.6 GB, 770 folders amounting for ~ 10k files.
I was said to upload a zip which is, indeed an acceptable solution in most cases.
But by comparing with WebDAV, we may possibly pinpoint a common underlying codepath that needs optimization?