One method to save a bit of memory could be to avoid to store the data in a hash of arrays. A simple Hash could reduce the necessary data. I'm imaginating a pseudo code like:

while (<IN>) {
    my ($key, $x, $y) = split;
    my @from_cache = split ' ', $cache{$key};
    $from_cache[0] += $x;
    $from_cache[1] += $y;
    $cache{$key} = join ' ', @from_cache;
}
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But of course, to use a database is the longterm right answer, as my solution is only a dirty hack :-)