I suppose:
If an input_array token (like N3) is in both A and B, then: CC0=1 and CC1 =1.
If an input_array token is in A but not in B, then "only 1 input is PI".
If an input_array token is not in A regardless whether it is in B or not, then: "this is a wire".

Looks odd to me...Is this logic correct? Is the case where input_array token is in B but not in A important? obviously in A but not in B is a special case.

Is any of Athananius' source helpful? Does it capture any of the logic you seek?

$ ./1.amee.pl 
N1: only 1 input is PI
N2: this is a wire
N6: this is a wire
N7: this is a wire
CC0[N3] = 1
CC1[N3] = 1
$ cat 1.amee.pl 
#!/usr/bin/perl
use 5.016;
use strict;
use warnings;
use List::Util qw( any );

my @input_array = qw( N1 N2 N3  N6  N7      );
my @input_A     = qw( N1 N3 N11 N11 N10 N16 );
my @input_B     = qw( N3 N6 N2  N7  N16 N19 );
my %primaryCC0;

for my $inputKey (@input_array)
{
    if (any { $_ eq $inputKey } @input_A)
    {
        if (any { $_ eq $inputKey } @input_B)
        {
            @{ $primaryCC0{$inputKey} } = (1, 1);
        }
        else
        {
            print "$inputKey: only 1 input is PI\n";
        }
    }
    else
    {
        print "$inputKey: this is a wire\n";
    }
}

for my $key (sort keys %primaryCC0)
{
    my ($CC0, $CC1)  = @{ $primaryCC0{$key} };
    print "CC0[$key] = $CC0\n";
    print "CC1[$key] = $CC1\n";
}

__END__
$
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What I find confusing about this script is non-descriptive output. For example, there is nothing in this problem that has anything to do with PI.