It looks to me like your problem is confusing local filesystem operations with remote ones. When you use the -l operator and readlink, it's looking in the local filesystem, not on the FTP server.

I don't think there's a standard way to determine whether a remote file is a symlink or not. You can use $ftp->dir and try to parse the output, or see if the FTP server you're using supports any nonstandard extensions that allow this (try sending a HELP command).