Both, glob and readdir will end up calling the same underlying C function

use strict;
use warnings;
use Cwd;
use Benchmark;

my $dir = 'c:/windows';

my ( @a1, @a2 );

timethese 1, {
    glob => sub {
        my $cwd = getcwd;
        chdir $dir;

        @a1 =  glob '*/*';

        chdir $cwd;
    },
    read => sub {
        my $cwd = getcwd;
        chdir $dir;

        opendir my $h, '.' or die;
        my @a = grep { $_ ne '.' and $_ ne '..' and -d $_ } readdir $h
+;
        for my $d ( @a ) {
            opendir my $hh, $d or next;
            push @a2, map "$d/$_", 
                      grep { $_ ne '.' and $_ ne '..' } 
                      readdir $hh;
        }

        chdir $cwd;
    }
};

use Test::More;
is $#a1, $#a2, 'array lengths are equal'
or do {
    use Test::Differences;
    eq_or_diff [ sort @a1 ], [ sort @a2 ], 'look deeper', 
        { context => 0 };;
};
done_testing;
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I don't care much about 7 (out of ~27e3) entries missing in one case (something to do with leading dot in a name), but I wonder if orders of magnitude speed difference is what OP is observing for his large tree. My Perl's latest Strawberry, + fast NVMe storage.

Benchmark: timing 1 iterations of glob, read...
      glob:  4 wallclock secs ( 0.30 usr +  3.34 sys =  3.64 CPU) @  0
+.27/s (n=1)
            (warning: too few iterations for a reliable count)
      read:  0 wallclock secs ( 0.03 usr +  0.06 sys =  0.09 CPU) @ 10
+.53/s (n=1)
            (warning: too few iterations for a reliable count)
not ok 1 - array lengths are equal
#   Failed test 'array lengths are equal'
#   at glob.pl line 39.
#          got: '27633'
#     expected: '27640'
not ok 2 - look deeper
#   Failed test 'look deeper'
#   at glob.pl line 41.
# +----+-----+----+-------------------------------------------+
# | Elt|Got  | Elt|Expected                                   |
# +----+-----+----+-------------------------------------------+
# |    |     * 656|  'INF/.NET CLR Data',                     *
# |    |     * 657|  'INF/.NET CLR Networking',               *
# |    |     * 658|  'INF/.NET CLR Networking 4.0.0.0',       *
# |    |     * 659|  'INF/.NET Data Provider for Oracle',     *
# |    |     * 660|  'INF/.NET Data Provider for SqlServer',  *
# |    |     * 661|  'INF/.NET Memory Cache 4.0',             *
# |    |     * 662|  'INF/.NETFramework',                     *
# +----+-----+----+-------------------------------------------+
1..2
# Looks like you failed 2 tests of 2.
[download]