If the count is all you need, you don't need of %hash at all:

my %count;

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

If McDarren is correct, and you want to keep track of all items, you should probably maintain an array inside $hash{$3} (and a variable rename would be good in this case), and in this case you would have the count "for free", just looking at how many elements each item has:

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{w
+hatever}
[download]

Note: untested code!