In general, Handy Backup provides interruption-free backup (e.g. you're backing up a 1gb file to FTP server when connection breaks, it will try to reconnect before canceling the transfer) and the speed generally depends on your bandwidth for those, although if you're talking about large amounts of small files, it depends on the specifics. If your FTP allows usage of absolute paths, there shouldn't be any speed issues with the backup, although for very large amounts of files we do recommend not putting them all in a single task.
I recommend trying it out and checking whether it suits your needs.