Nextcloudpi slow with many small files (rpi3 non plus)

Unfortunately the problem is your Pi 3.
Webdav has trouble with moving tons of small files, but the main limitation here is your hardware.

Do it! Absolutely the better choice. You can also mount this external location to your Pi 3 (see documentation or search the forum for instructions) and keep using Nextcloud while keeping your data available over Samba / NFS (depending on your router config).