Depends upon your filing system, but 2 x 2-digits means a max of 100 in the lower levels and 10,000 in the top. 2 x 3-digit, gives 1000 in teh lower levels and 100 in the top. Every filesystem I am aware of will handle those numbers with ease.

The latter probably works better for performance, but you'd have to do a few tests to be sure.

On my system it is much of a muchness at around 3 milliseconds per lookup/increment either way:

#! perl -slw
use strict;
use Time::HiRes qw[ time ];

mkdir 'myroot';
for my $l1 ( '00' .. '09' ) {
    mkdir "myroot/$l1";
    for my $l2 ( '00' .. '09' ) {
        mkdir "myroot/$l1/$l2";
        mkdir "myroot/$l1/$l2/$l1$l2$_" for  '000' .. '999';
        mkdir "myroot/$l1/$l2/$l1$l2$_/1" for '000' .. '999';
    }
}

my $start = time;
for( 1 .. 1000 ) {
   my $id = sprintf "%02u%02u%03u", int( rand 10 ), int( rand 10 ), in
+t( rand 1000 );
   my( $l1, $l2 ) = unpack 'a2a2', $id;
   opendir D, "myroot/$l1/$l2/$id/";
   readdir D; readdir D; ## get rid of '.' & '..'
   my $count = readdir D;
   rename "myroot/$l1/$l2/$id/" . $count, "myroot/$l1/$l2/$id/" . ++$c
+ount
      or warn "$! : $id : $count";
   closedir D;
}
printf "2x2x7 took %f secs/lookup&increment\n", ( time() - $start ) / 
+1000;

system "rd /q /s myroot";

mkdir 'myroot';
for my $l1 ( '000' .. '009' ) {
    mkdir "myroot/$l1";
    for my $l2 ( '000' .. '009' ) {
        mkdir "myroot/$l1/$l2";
        mkdir "myroot/$l1/$l2/$l1$l2$_" for  '0' .. '9';
        mkdir "myroot/$l1/$l2/$l1$l2$_/1" for '0' .. '9';
    }
}

$start = time;
for( 1 .. 1000 ) {
   my $id = sprintf "%03u%03u%01u", int( rand 10 ), int( rand 10 ), in
+t( rand 10 );
   my( $l1, $l2 ) = unpack 'a3a3', $id;
   opendir D, "myroot/$l1/$l2/$id/" or warn "$! : myroot/$l1/$l2/$id/"
+;
   readdir D; readdir D; ## get rid of '.' & '..'
   my $count = readdir D;
   rename "myroot/$l1/$l2/$id/" . $count, "myroot/$l1/$l2/$id/" . ++$c
+ount
      or warn "$! : $id : $count";
   closedir D;
}
printf "3x3x7 took %f secs/lookup&increment\n", ( time() - $start ) / 
+1000;

system "rd /q /s myroot";

__END__
C:\test>1032393
2x2x7 took 0.002671 secs/lookup&increment
3x3x7 took 0.002761 secs/lookup&increment

C:\test>1032393
2x2x7 took 0.002628 secs/lookup&increment
3x3x7 took 0.003111 secs/lookup&increment
[download]

BTW: Please note the additional readdir D; readdir D; ## get rid of '.' & '..' which I forgot above.