As long as you know what the difference is, it doesn't really matter much which one you use.

Under some circumstances, it might be more "natural" to use a plain hash, for example when Perl syntactically requires a hash, as in keys %hash (because then you don't have to write keys %$hash to dereference a hashref).  In other cases, it might be more natural to use a hashref in the first place, e.g. when you want to pass it to a function without copying/flattening it (so you can say func($hash) instead of func(\%hash) ).  But ultimately, it's just a matter of personal preference.

P.S.: the arrows between indices are optional (because there's nothing to disambiguate — nested structures are always references), i.e. your sample case could also be written as

$a[0][2]{foo}       # plain array
$r->[0][2]{foo}     # array ref
[download]