In your "Without References" example, don't you need  return ++$arg;?
(and a semicolon after shift?)
Also, consider the following:

sub increment {
     ++$_[0];
}
$num=0;
increment($num);
print $num,"\n";
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which shows that args are passed "by reference" by default. Of course, it may not be good style to alter @_ in this way, but the point is that you don't need to pass a reference to alter the argument inside the sub.
(Updated to make less confusing.)