Am i missing something?

This is probably closer to what you want:

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

my $sitedb = {
    'User1' => {
        '7' => {
            'HOST'             => 'foobar.baz.com',
            'REMOTE_DIRECTORY' => '/tmp/user1_test',
            'JOB_ID'           => '7',
            'LOCAL_DIRECTORY'  => 'to-user',
            'MAIL'             => 'baz@foobar.com',
            'SITE'             => 'user1',
            'PORT'             => '21'
        },
        '2' => {
            'HOST'             => 'foobar.baz.com',
            'REMOTE_DIRECTORY' => '/tmp/user1_test',
            'JOB_ID'           => '7',
            'LOCAL_DIRECTORY'  => 'to-user',
            'MAIL'             => 'baz1@foobar.com',
            'SITE'             => 'user1',
            'PORT'             => '21'
        }
    },
    'User2' => {
        '6' => {
            'HOST'             => 'foobar.baz.com',
            'REMOTE_DIRECTORY' => '/tmp/user2_test',
            'JOB_ID'           => '7',
            'LOCAL_DIRECTORY'  => 'to-user',
            'MAIL'             => 'baz2@foobar.com',
            'SITE'             => 'user1',
            'PORT'             => '21'
        }
    }
};


foreach my $site_name ( keys %{ $sitedb } ) {
    print "Checking $site_name ... \n";

    foreach my $subkey ( keys %{ $sitedb->{$site_name} } ) {
        my @jobid = $sitedb->{$site_name}{$subkey};
        print Dumper(@jobid);
        print "Job ID: @jobid\n";
    }
}

__END__

Checking User1 ...
$VAR1 = {
          'HOST' => 'foobar.baz.com',
          'JOB_ID' => '7',
          'LOCAL_DIRECTORY' => 'to-user',
          'MAIL' => 'baz@foobar.com',
          'PORT' => '21',
          'REMOTE_DIRECTORY' => '/tmp/user1_test',
          'SITE' => 'user1'
        };
Job ID: HASH(0x60b220)
$VAR1 = {
          'HOST' => 'foobar.baz.com',
          'JOB_ID' => '7',
          'LOCAL_DIRECTORY' => 'to-user',
          'MAIL' => 'baz1@foobar.com',
          'PORT' => '21',
          'REMOTE_DIRECTORY' => '/tmp/user1_test',
          'SITE' => 'user1'
        };
Job ID: HASH(0x661ff0)
Checking User2 ...
$VAR1 = {
          'HOST' => 'foobar.baz.com',
          'JOB_ID' => '7',
          'LOCAL_DIRECTORY' => 'to-user',
          'MAIL' => 'baz2@foobar.com',
          'PORT' => '21',
          'REMOTE_DIRECTORY' => '/tmp/user2_test',
          'SITE' => 'user1'
        };
Job ID: HASH(0x624400)
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