You're storing your data in the wrong structures.

You never use the values in the hash %a; you never use it's lookup ability; and you want to iterate it in order.

Your arrays @a1 and @a2:

1. you want to use as lookup table and have to iterate the whole thing each time with grep.
2. Dont care about the order, only the presence.
3. Iterate, only for the greps, never for the ordering.

By reversing the type of structures used you get:

#! perl -slw
use strict;

my %a=( AA=>'Y', BB=>'Y', CC=>'Y', DD=>'Y', EE=>'Y', FF=>'Y' );
my @a1=('AA','DD','EE');
my @a2=('AA','BB','CC','FF');

my @a = sort keys %a;
my %a1; @a1{ @a1 } = ();
my %a2; @a2{ @a2 } = ();

print join ',', map{ exists $a1{ $_ } ? $_ : '##' } @a;
print join ',', map{ exists $a2{ $_ } ? $_ : '##' } @a;

__END__
[11:44:17.92] P:\test>413151
AA,##,##,DD,EE,##
AA,BB,CC,##,##,FF
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