Note that I changed your outer %struct squigglies to parens. I've left some debug prints in the following code for illustrative purposes:

#!/usr/local/bin/perl
use strict;

my %struct = (
        row1 => { key0 => 'val0', key1 => 'val2', keyX => 'valX' },
        row2 => { key0 => 'val0', key1 => 'val1', keyX => 'valX' },
        row3 => { key0 => 'val0', key1 => 'val1', keyX => 'valY' },
        row9 => { key0 => 'val0', key1 => 'val1', keyX => 'valY' },
        rowX => { key0 => 'val0', key1 => 'val1', keyX => 'valX' }
   );

my %ndxhash = ();

print "Before deletions:\n";
foreach my $row (keys(%struct)) {
   print "\$row: $row";
   print "   key0: $struct{$row}{key0} ";
   print "   key1: $struct{$row}{key1} ";
   print "   keyX: $struct{$row}{keyX} \n";
   ## build a key to determine a uniqueness in %ndxhash
   my $ndxkey = Trim($struct{$row}{key0}) .
                Trim($struct{$row}{key1}) .
                Trim($struct{$row}{keyX});
   if (exists $ndxhash{$ndxkey}) {
      ## this one is a duplicate
      delete $struct{$row};
   } else {
      ## this is a unique one, add it to the %ndxhash
      $ndxhash{$ndxkey} = 1;
   }
}

print "\n\nAfter deletions\n\n";
foreach my $row (keys(%struct)) {
   print "\$row: $row";
   print "   key0: $struct{$row}{key0} ";
   print "   key1: $struct{$row}{key1} ";
   print "   keyX: $struct{$row}{keyX} \n";
}

sub Trim {
   my $InVar = shift;
   for ($InVar) {
       s/^\s+//;
       s/\s+$//;
   }

   if (! $InVar) {
      $InVar = " ";
   }
   return $InVar;
}
[download]

Before Deletions:
$row: rowX   key0: val0    key1: val1    keyX: valX
$row: row9   key0: val0    key1: val1    keyX: valY
$row: row1   key0: val0    key1: val2    keyX: valX
$row: row2   key0: val0    key1: val1    keyX: valX
$row: row3   key0: val0    key1: val1    keyX: valY

After Deletions
$row: rowX   key0: val0    key1: val1    keyX: valX
$row: row9   key0: val0    key1: val1    keyX: valY
$row: row1   key0: val0    key1: val2    keyX: valX
[download]

Update: removed unused variable in Trim sub

Note that I changed your outer %struct squigglies to parens
]- yep... I'm making this mistake very often :")

Thanx alot ....