my %count;

while (<FILE>){
 
 next unless /something/; 
 if (/<LONG REGEX>/){
   
    $count{$3}++ if $3;
 }
}

##</code><code>##

my %hashes_for;  # More sensible name

while (<FILE>){
 
 next unless /something/; 
 if (/<LONG REGEX>/){
   
   push @{$hashes_for{$3}}, {
        sig => $1,
        src => $3,
        proto => $2,
        dst => $4,
        port => $5,
   };
 }
}

# You can now use scalar(@{$hashes_for{whatever}}) instead of $count{whatever}