Since you are already passing by reference, any changes you make in the sub are reflected out of the sub:

use warnings;
use strict;
use Data::Dumper;

$Data::Dumper::Sortkeys = 1;

my %palette;

$palette{'palette_info'}[0]    = 128;
$palette{'mask_info'}[0]       = 0;
$palette{'shade_stencil_mask'} = 99 ;

print Dumper(\%palette);

writeCmd(111, \%palette, 222, 333);

print Dumper(\%palette);


sub writeCmd {
    my $command = shift;
    my $pal     = shift;
    my $address = shift;
    my $length  = shift;

    $pal->{'palette_info'}[0] = 444;
    $pal->{'shade_stencil_mask'} = 234;
}


__END__


$VAR1 = {
          'mask_info' => [
                           0
                         ],
          'palette_info' => [
                              128
                            ],
          'shade_stencil_mask' => 99
        };
$VAR1 = {
          'mask_info' => [
                           0
                         ],
          'palette_info' => [
                              444
                            ],
          'shade_stencil_mask' => 234
        };
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