• adding chomp to get rid of the extra newlines that are left on the $val
• removing the spaces, along with the commas, on the split, so they don't end up as part of the hash indices
• using a canonical form for the table index, so that "ob1,bo2" and "ob2,ob1" go in the same bin.
• just one hash for which rows and columns are present
• print "-" if there's no entry

You were well on your way, but the first two on this list can confuse things enough that you can't see the rest. That's the way it happens, it's the things you're not looking at that get you.

use strict;
my %table;
my %rows_cols;
my %cols;

for(<DATA>) {
   chomp;
  my($row,$col,$val) = split ', *';
  if ($row>$col) {
     ($row,$col) = ($col,$row);
   }
  $table{$row}{$col} = $val;
  $rows_cols{$row}++;
  $rows_cols{$col}++;
}

for my $col (sort keys %rows_cols) {
  print "\t$col";
}
print "\n";

my $val;
for my $row (sort keys %rows_cols) {
  print "$row\t";
  for my $col (sort keys %rows_cols) {

    if (defined $table{$row}{$col}) {
       print $table{$row}{$col};
    }
    elsif (defined $table{$col}{$row}) {
       print $table{$col}{$row};
    }
    else {
       print "-";
    }
    print "\t";
  }
  print "\n";
}
__END__
ob1, ob2, 34
ob1, ob3, 56
ob1, ob4, 12
ob1, ob5, 78
ob1, ob6, 23
ob3, ob1, 56
ob7, ob1, 23
ob8, ob1, 12
ob9, ob1, 90
ob3, ob2, 87
[download]

        ob1     ob2     ob3     ob4     ob5     ob6     ob7     ob8   
+  ob9
ob1     -       34      56      12      78      23      23      12    
+  90

ob2     34      -       87      -       -       -       -       -     
+  -

ob3     56      87      -       -       -       -       -       -     
+  -

ob4     12      -       -       -       -       -       -       -     
+  -

ob5     78      -       -       -       -       -       -       -     
+  -

ob6     23      -       -       -       -       -       -       -     
+  -

ob7     23      -       -       -       -       -       -       -     
+  -

ob8     12      -       -       -       -       -       -       -     
+  -

ob9     90      -       -       -       -       -       -       -     
+  -
[download]