A hash of hash might be a possible solution. Here I didn't keep a separate frequency but generated a frequency for each $tag1 as the value to the hash.

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper qw(Dumper);
use List::Util 'sum';

open my $fh, '<', \<<EOF;
The    DT    the
International    NN    International
for    IN    for
well    NN    well
preparation    NN    preparation
preparation    NN    preparation
in    IN    in
conference    NN    conference
conference    NN    conference
conferences    NN    conference
good    VVG    good
EOF

my %hash;
while (<$fh>) {
    chomp;
    my ($tag1, $tag2, $tag3) = split /\t/;
    
    if ($tag2 =~/NN/) {
        $hash{$tag3}{$tag1}++;
    }
}
print Dumper \%hash;

for my $tag (keys %hash) {
    printf "%s freq: %d\n", $tag, sum values %{ $hash{$tag} };    
}
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Output:

$VAR1 = {
          'well' => {
                      'well' => 1
                    },
          'International' => {
                               'International' => 1
                             },
          'conference' => {
                            'conference' => 2,
                            'conferences' => 1
                          },
          'preparation' => {
                             'preparation' => 2
                           }
        };

well freq: 1
International freq: 1
conference freq: 3
preparation freq: 2
[download]