my @down = keys %matrix;
my @across = do {my %s; grep {!$s{$_}++} map {keys %$_} values %matrix};

my $l = 0;
$l < length ($_) and $l = length $_ for @down, @across;

print " " x $l;
printf "  %-${l}s", $_ for @across;
print "\n";
foreach my $d (@down) {
    printf "%-${l}s", $d;
    printf "  %${l}d", $matrix{$d}{$_} || 0 for @across;
    print "\n";
}