It is a common practice, although not always the best idea. I often see $r or $ret (or @r, %r, @ret, %ret, etc) as the name of whatever variable will ultimately contain the value(s) to be returned. Often, the variable should instead be named in a way that makes the name itself self-document its contents or its use. I cannot tell if this would be one of those cases.

Untested, equivalent code (just because I read via refactoring):

sub read_dt2 {
    my ($path) = @_;
    open my $IFH, '<', $path
        or die "cannot open file '$path': $!";

    my %mysterious_hash_keyed_by_nucleotide;
    for my $nucleotide ( qw( A C G T ) ) {
        local $_ = <$IFH>;
        $mysterious_hash_keyed_by_nucleotide{$nucleotide} = [split];
    }
    close $IFH
        or warn "cannot close file '$path': $!";
    return \%mysterious_hash_keyed_by_nucleotide;
}
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