I don't think $line will every be empty - you probably ought to chomp it, or test for non-whitespace.

And you still have unnecessary tests in your if-elsif. For example, if $score is NOT greater-than $warnrate, it IS NECESSARILY less-than-or-equal-to $warnrate.

Consider:

use strict;

my $radio      = $ARGV[0];
my $warnrate   = $ARGV[1];
my $critrate   = $ARGV[2];
chomp(my $line = `/usr/bin/snmpwalk -v1 -c PTsnmp $radio .1.3.6.1.4.1.
+5454.1.40.2.4.0`;
if ($line !~ /\S/) {
   print "snmpwalk returned nothing, timeout likely occurred.\n";
   exit 3;
} elsif ($critrate > $warnrate) {
   print "Make sure your critical value is less than or equal to your 
+warning value.\n";
   exit 5;
} else {
   my $score         = (split(' ', $line))[3];
   my ($msg,$status) = $score > $warnrate   ? ('OK',0) 
                     : ( $score > $critrate ? ('WARNING',1) 
                     : ('CRITICAL',2));
   print "$msg, rf is $score. |Mbps=$score\n";
   exit $status;
}
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