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

    foreach my $subkey (keys %{$site_db{$site_name}}) {
        my @jobid = $site_db{$site_name}{$subkey};
        print Dumper(@jobid);
        print "Job ID: @jobid\n";
    }
    }
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You are using %$sitedb in the outer loop and $site_db in the inner loop.    Also, you are not dereferencing the hash keys in the inner loop.