1) You keep replacing the array referenced by $main{$mn."-join"}{$msec} instead of adding to it.

2) last INNER if (length($join) > 2); is a bad way of not treating your outputs as inputs.

use strict;
use warnings;

use Data::Dumper;

my %main = ( 'main1' => {'m1sec1'=> ['A','B','C'],},
             'main2' => {'m2sec1'=> ['D','E','F'],},);

my %seed = ( 'seed' => {'seed1'=> ['X','Y','Z']},);

# Keep output seperate for now to
# avoid treating outputs as inputs.
my %joined;

foreach  my $sd ( keys %seed )
{
    foreach  my $sdsub ( sort keys %{$seed{$sd}} )
    {
        foreach  my $valseed ( @{$seed{$sd}{$sdsub}}  )
        {
            foreach  my $mn ( keys %main )
            {
                foreach  my $msec ( sort keys %{$main{$mn}} )
                {
                    # Create hash if it doesn't exist.
                    $joined{$mn."-join"} ||= {};
                    
                    # Create array if it doesn't exist.
                    $joined{$mn."-join"}{$msec} ||= [];
                    
                    my $store = $joined{$mn."-join"}{$msec};


                    foreach  my $valmain( @{$main{$mn}{$msec}}  )
                    {
                        push @$store, $valmain.$valseed;
                    }
                }
            }
        }
    }
}

# Combine inputs and outputs.
%main = (%main, %joined);

print Dumper \%main ;
[download]

Update: It's a bit cleaner if you change the order of the loops, putting outputs at the top level.

use strict;
use warnings;

use Data::Dumper;

my %main = ( 'main1' => {'m1sec1'=> ['A','B','C'],},
             'main2' => {'m2sec1'=> ['D','E','F'],},);

my %seed = ( 'seed' => {'seed1'=> ['X','Y','Z']},);

foreach  my $mn ( keys %main )
{
    my $joined = $main{"$mn-join"} = {};

    foreach  my $msec ( sort keys %{$main{$mn}} )
    {
        my $store = $joined->{$msec} = [];

        foreach  my $valmain( @{$main{$mn}{$msec}}  )
        {
            foreach  my $sd ( keys %seed )
            {
                foreach  my $sdsub ( sort keys %{$seed{$sd}} )
                {
                    foreach  my $valseed ( @{$seed{$sd}{$sdsub}}  )
                    {
                            push @$store, $valmain.$valseed;
                    }
                }
            }
        }
    }
}

print Dumper \%main ;
[download]

Update: It seems wierd to me that %seed is a HoHoA instead of just an array, since the entire contents of the HoHoA are treated as a single array. This generates the same output (and is probably slightly faster):

use strict;
use warnings;

use Data::Dumper;


my %main = ( 'main1' => {'m1sec1'=> ['A','B','C'],},
             'main2' => {'m2sec1'=> ['D','E','F'],},);

my %seed = ( 'seed' => {'seed1'=> ['X','Y','Z']},);


my @seed;  # Flattened %seed.

foreach  my $sd ( keys %seed )
{
    foreach  my $sdsub ( sort keys %{$seed{$sd}} )
    {
        push @seed, @{$seed{$sd}{$sdsub}};
    }
}


foreach  my $mn ( keys %main )
{
    my $joined = $main{"$mn-join"} = {};

    foreach  my $msec ( sort keys %{$main{$mn}} )
    {
        my $store = $joined->{$msec} = [];

        foreach  my $valmain( @{$main{$mn}{$msec}}  )
        {
            foreach  my $valseed ( @seed  )
            {
                push @$store, $valmain.$valseed;
            }
        }
    }
}


print Dumper \%main ;
[download]

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