The sub below uses an external hash of references to the elements of $data[1], called %data_refs_hash. Using that hash you can do the increment directly. You only need to scan through the array when you're adding a new key (and you only need to do that if you're keeping the keys in order, if not, leave out the while() scan and just push the new values on the end instead of splicing them.)

sub IncrData {
   my $key = shift;

   if (exists $data_refs_hash{$key} ) { # if there's a hash entry
      ${$data_refs_hash{$key}}++;       # increment it
   }
   else {   # otherwise, find a spot and put one in
      my $idx = 0;
      my $endIdx = scalar(@{$data[0]});
      while ($idx < $endIdx && $data[0][$idx] < $key) {
         $idx++;
      }
      splice(@{$data[0]},$idx,0,$key);
      splice(@{$data[1]},$idx,0,1);
      $data_refs_hash{$key} = \$data[1][$idx];
   }
   # if you need to update the sort each time, then do
   @{$data[2]} = sort { $a <=> $b } @{$data[1]};
   # but you shouldn't update it until you're going to use it, 
   # since it's expensive to sort for every increment

} # IncrData
[download]

my @data = (
           ["1.6","2.2","3.4","3.6","5.4","6.2","7.1", "8.1", "9.0"],
           [    1,    2,    5,    6,    3,  15,    4,     3,     4],
           [ sort { $a <=> $b } (1, 2, 5, 6, 3, 15, 4, 3, 4) ]
         );

# create a hash of refs to the things you want to updated.
# This is only needed for the example, so that we can
# use the ininialized array above. Normally, the hash is just updated 
# each time a new element is added to the arrays in IcrData().
for $idx (0..$#{$data[0]} ) {
   $data_refs_hash{$data[0][$idx]} = \$data[1][$idx];
}

print join(", ", @{$data[1]}), "\n";

IncrData("3.4");
IncrData("3.5");
IncrData("9.5");
IncrData("1.1");
IncrData("9.5");

print "\n";
print join(", ", @{$data[0]}), "\n";
print join(", ", @{$data[1]}), "\n";
print join(", ", @{$data[2]}), "\n";

#produces 
1.1, 1.6, 2.2, 3.4, 3.5, 3.6, 5.4, 6.2, 7.1, 8.1, 9.0, 9.5
1, 1, 2, 6, 1, 6, 3, 15, 4, 3, 4, 2
1, 1, 1, 2, 2, 3, 3, 4, 4, 6, 6, 15
[download]