I'd be inclined to maximize the use of distinct subroutines for specific subsets of data, as well as using more hashes to organize things according to types and labels. Here's how I would try to structure the first part of the OP code. (I think the array idea mentioned above will help a lot with the rest.)

I have no way of testing this proposal in a relevant way, but I think the layout is basically in line with what you're trying to do. (Note that I'm renaming your "$AO_ESMEdep_error" to a hash key spelled "AO_userdep_error", to maintain parallelism between the GSM and SMPP conditions - I hope that doesn't warp things too much for you (the parallelism is worth it, I think).

my %tallies;
my %errors = {
    userdep_error => \@subscriber_error,
    network_error => \@network_error,
    system_error => \@system_error,
};

sub do_GSM
{
    my $fields = shift;
 
    if ( $$fields[9] eq 'MSubmit' ) {
        $tallies{MO_count}++;
        if ( $$fields[7] eq 'MsgAccepted' ) {
            $tallies{MO_success]++;
        }
    }
    if ( $$fields[13] eq 'SMPP' ) {
        $tallies{AT}++;
    }

    for my $type ( keys %errors ) {
        if ( any { /^\Q$$fields[11]\E$/ } @{$errors{$type}} ) {
            $tallies{"MO_$type"}++;
        }
    }
}

sub do_SMPP
{
    my $fields = shift;

    if ( $$fields[9] eq 'ESubmit' ) {
        $$tallies{AO_count}++;
        if ( $$fields[7] eq 'MsgAccepted' ) {
            $tallies{AO_success}++;
        }
    }
    if ( $$fields[11] =~ /SMSC/ ) {
        for my $type ( keys %errors ) {
            if ( any { /^\Q$$fields[11]\E$/ } @{$errors{$type}} ) {
                $tallies{"AO_$type"}++;
            }
        }
    }
}

my %subs = ( GSM => \&do_GSM, SMPP => \&do_SMPP );

foreach my $Intermediate_file (@Intermediate_files)
{
    unless ( open (INTER, $Intermediate_file )) {
        warn "open failed for $Intermediate_file\n";
        next;
    }
    while (<INTER>)
    {
        chomp;
        my @fields = split(/\|/);
        &{$subs{$fields[12]}}( \@fields );
    }
}
print "Completed the Imtermediate section....\n";
...
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I also altered the handling of open failures and shortened the variable names.