Converting your list just screams "map" to me, so that's the kind of solution I was shooting for.

use Data::Dumper;

my @data = qw( 000- 0101 011- 1-0- );
print Dumper(\@data);

@data = map { bits($_) } @data;
print Dumper(\@data);

sub bits {
    my $str = shift;
    if ($str =~ /-/) {
        my ($zero, $one) = ( $str, $str );
        $zero =~ s/-/0/;
        $one =~ s/-/1/;
        return ( bits( $zero ), bits( $one ) );
    } else {
        return $str;
    }
}
__END__
$VAR1 = [
          '000-',
          '0101',
          '011-',
          '1-0-'
        ];
$VAR1 = [
          '0000',
          '0001',
          '0101',
          '0110',
          '0111',
          '1000',
          '1001',
          '1100',
          '1101'
        ];
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