The following first captures the file names in named.conf and places them into a hash. It then globs the zonefiles' directory, and attempts to find each listed file from that directory in the hash. If the file name's not in the hash, it's pushed onto @unlistedFiles for later processing:

use strict;
use warnings;

my ( %named_conf, @unlistedFiles );

open my $fh, '<', 'named.conf' or die $!;
/\s+file\s+"([^"]+)/ and $named_conf{$1}++ for <$fh>;
close $fh;

chdir 'zonefiles' or die $!;
!defined $named_conf{$_} and push @unlistedFiles, $_ for <db.*>;

print "$_\n" for @unlistedFiles;
[download]

Files in zonefiles directory:

db.127.0.0
db.brian.com
db.cache
db.test.com
db.what
db.why
[download]

Output using your named.conf:

db.what
db.why
[download]

Hope this helps!