You might be interested in Building Regex Alternations Dynamically so that you don't have to loop over your IDs.

use warnings;
use strict;
use Data::Dump;

my @ids = ("a", "b", "c", "d", "e", "f", "g",);

my ($regex) = map {qr/$_/} join '|', map {quotemeta}
    sort { length $b <=> length $a or $a cmp $b } @ids;

my %counts = map { $_ => 0 } @ids;
while (<DATA>) {
    if ( my ($id) = /($regex)/ ) {
        $counts{$id}++;
    }
}

dd \%counts;
# outputs "{ a => 1, b => 2, c => 2, d => 3, e => 0, f => 3, g => 0 }"

__DATA__
a
b
b
NO ID HERE
c
c
d
d
d
f
f
f
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