my %matrix = ('R-Linux'  => {confdir=>'abc'},
              'R-Solaris'=> {scriptpath=>'def'});
sub item {
  my ($os,$what,$value) = @_;
  $matrix{$os}{$what} = $value if 3==@_;
  return $matrix{$os}{$what};
}

sub delete_item {
  my ($os,$what) = @_;
  delete $matrix{$os}{$what};
}

...