You can gain a tad more by truncating the 64-bit int to 6 bytes, but you're into a world of diminishing returns:

#! perl -slw
use strict;
#use Math::Random::MT qw[ rand ];
use Devel::Size qw[ total_size ];

our $S //= 1; srand( $S );

my %hash;
for( 1 .. 1e6 ) {
    my( $x, $y, $z ) = ( int( rand 20 ), int( rand 1.2e6 ), int( rand 
+1.2e6 ) );
#    ++$hash{ $x }{ $y }{ $z };
#    ++$hash{ join $;, $x, $y, $z };
#    ++$hash{ pack 'Q', $x * 1.2e6**2 + $y * 1.2e6 + $z };
    ++$hash{ unpack 'A6', pack 'Q', $x * 1.2e6**2 + $y * 1.2e6 + $z };
}
print total_size( \%hash ), ' ', scalar keys %hash;

__END__
    ++$hash{ $x }{ $y }{ $z };                                        
+      269 897 378
    ++$hash{ join $;, $x, $y, $z };                                   
+      106 036 953         40%
    ++$hash{ pack 'Q', $x * 1.2e6**2 + $y * 1.2e6 + $z };             
+       98 388 672         36.5%
    ++$hash{ unpack 'A6', pack 'Q', $x * 1.2e6**2 + $y * 1.2e6 + $z };
+       96 193 539         35.6%
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Beyond that, if it is still a problem, print the triplets to stdout and pipe the results through your system sort and then into a another perl script that counts them:

C:\test>perl -E"say join ' ', int( rand 20 ), sort{ $a<=>$b } int( ran
+d 1.2e6 ), int( rand 1.2e6 ) for 1 .. 1e6" 
| sort 
| perl -nle"if($last eq $_){ ++$n }else{ print qq[$last : $n];$n=1} $l
+ast=$_" 
| wc -l
 999978
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