You could use a hash to hold onto the hashes with very little extra work:

sub GetStats {
        my $ref_files = shift @_;
        my %lkup_by = (who => {}, how => {}, from => {}, ftp => {});

        foreach my $file (@$ref_files) {
                ...
                while (<LAST>) {
                        ...
                        $lkup_by{who}{$file}{$who}++;
                        $lkup_by{from}{$file}{$from}++;
                        if ($how eq "ftp") {
                                $lkup_by{ftp}{$file}{$who}++;
                        }
                }
                close (LAST);
        }
        return ($lkup_by{who}, $lkup_by{from}, $lkup_by{ftp});
}
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I don't see where you need to get at the names however. Note too that you don't need to interpolate variables into strings, just use them directly.