That is because this code:

if  (!($_ =~ /$search/))  {  
   print "\nsubstring <$search> NOT found\n";
}
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is executed outside the loop. So it will print the message always, except for the case when the last line contains the searchword. You have to use a flag.

my $found;
my $counter;

for (@line)
{
  $counter++;
 
  if  ($_ =~ /$search/i)  
  {  
    print "\nLine that matched <$search> found on line $counter\n"; 
    print "$_\n";
    $found++;
  }
}
        
if  ( $found )  
{  
  print "$count found words total\n";
}
else
{
  print "\nsubstring <$search> NOT found\n";
}
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