my %SMPP_count;

foreach my $file (@files)
{               
        open (FILE,"$file"); 
        while(<FILE>)   
        {               
                next unless /\b(?:GSM|SMPP)\b/; # avoid uninteresting lines
                chomp;
                my @ary  = (split /\s|\|/, $_) [3,21,24];
                my $time = (split ' ', $ary[0])[4]; # first element ist timestamp, right?
                $SMPP_count{$time}++ if  $ary[0] eq $stamp and $ary[1] eq "Submit" and $ary[2] =~ /(GSM|SMPP)/;
        };
}

# now iterate over the keys of the hash to make up your sums

for my $time ( sort keys %SMPP_count) {
    my $sum = $SMPP_count{$time};
    ...
}