That's correct; the Net::SSH::Perl documentation says the first item of the list returned by $ssh->cmd is the entire output of the command.

You can use split to split the output into lines:

my ($out, $err1, $exit2) = $ssh->cmd("df -k");

for my $line (split /\n/, $out) {
    print "$cnt: $line\n";
    $cnt++;
}
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If the output is potentially large (this doesn't apply for df -k but might be useful to know in the future), and you want to avoid copying all the data like split does you might do something like:

my $cnt = 1;
while ($out =~ /\G(.+)\n?|\G\n/g) {
    print "$cnt: $1\n";
    $cnt++;
}
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or if you're certain the last line ends in a newline, you can simplify the pattern to /\G.*\n/g

And finally it might be more efficient to use index and substr, but it would certainly yield more complex code.