Probably a better thought out solution could be made, but I think this may be what you're after.

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

my %hash = ( 
'abc,def' => {
               ',,,item4' => 1,
               'item1,,,' => 1,
               ',item2,,' => 1
              },
'kln,mno' => {
               ',,,item4' => 1,
               'item1,,,' => 1
              },
);

my %new_hash;
for my $key (keys %hash) {
    my @array;
    for (keys %{ $hash{$key}}) {
        my ($lead_comma,$item) = /^(,*)([^,]+)/;
        $array[ length $lead_comma ] = $item;
    }
    $new_hash{$key} = \@array;
}
use Data::Dumper; print Dumper \%new_hash;

__END__
output from Data::Dumper

$VAR1 = {
          'abc,def' => [
                         'item1',
                         'item2',
                         undef,
                         'item4'
                       ],
          'kln,mno' => [
                         'item1',
                         undef,
                         undef,
                         'item4'
                       ]
        };
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