Just check if the A-B exists before adding B-A.

my %hash2 =(
    '1' => 2,
    '3' => 5,
    '4' => 2,
);

my %spair = ();

for my $si (keys %hash2) {
    for my $sn (keys %hash2) {     
      next if exists $spair{$sn."-".$si};
        $spair{$si."-".$sn} = ($si == $sn)? $hash2{$si} : $hash2{$si}*
+$hash2{$sn};
    }
}
use Data::Dumper;
print Dumper \%spair;

__DATA__
$VAR1 = {
          '3-3' => 5,
          '1-1' => 2,
          '3-4' => '10',
          '1-3' => '10',
          '1-4' => '4',
          '4-4' => 2
        };
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