That doesn't seem to be the case for me:

#!/usr/bin/perl -l

use strict;
use warnings;

my %hoh=( h => {foo=>1}, g => {bar=>2} );
print scalar keys %hoh;
print scalar keys %{ $hoh{h} };

undef %hoh;
print scalar keys %hoh;
print scalar keys %{ $hoh{h} };

__END__
[download]

I get:

2
1
0
0
[download]

But I wouldn't use undef on aggregates anyway.