Instead of deleting from an array I am using grep. The disadvantage is that this involves some copying (at least twice) so it involves some time and memory.

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

sub hdb_prune {
  my $arr = shift;
  my @res = grep { not ref $_ or hdb_prune( $_ ) } @$arr;
  return () if not @res;
  @$arr = @res;
  return $arr;
}

my @arr = ( 1, 2, [], 4, [ 11, 22, [], 44, [ 12, []] ] );
hdb_prune( \@arr );
print Dumper \@arr;
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