In general I agree with you. Though in practice when the returned value is NA the test will throw an error anyway, so the problem will be caught. A stronger reason to prefer === is that x == false can (in theory) be true even if x is not the false singleton, so === is a stricter way to check the behavior of a function. More generally, === is useful since it allows checking the type (but of course it can only be used for immutables).
Pull requests to replace == with === where applicable would likely be welcome in most packages.