use strict;

my %hash1 = (1=>[5,4,3,2,1],
             2=>[1,2,3],
             3=>[8,9]);

my %hash2 = (1=>[6,5,4,3,2],
             3=>[4,5]);

foreach my $key1 (keys %hash1) {
   if (exists $hash2{$key1}) {
      foreach my $ss (0..@{$hash1{$key1}}) {
         ## do subtraction here using $ss as subscripts: 
         ## my $data1 = $hash1{$key1}[$ss] - $hash2{$key1}[$ss];
         ## it's not clear from your code why you're subtracting
         ## keys from values.
      }
   }
}