I would mount encrypted remote with --vfs-cache-mode full --vfs-read-chunk-size 1M and use something like fclones.
then you could run:
fclones group . --max-prefix-size 1MB --max-suffix-size 1MB --skip-content-hash
It would only read and hash 2MB (1MB from the beginning and end of a file) from every suspected duplicate (where length is the same) and thanks to --vfs-read-chunk-size 1M mount option only 2MB are read from remote per file.