Are philosophers today misunderstanding 'emptiness' because of a new metaphysics?

One can hardly say "philosophers today", as philosophy itself is a wide field of activities; it can mean academic philosophy (which is publish-or-perish style of life, plus perhaps thinking "I am special because I do something which is profound and special" -- but that's the same for physicists or biologists) or conceptual reflection of experience. But it matters what experience is reflected, at what level, and what is the reflection supposed to bring.

So I will discuss philosophy as something extra-theoretical.

I happen to disagree with Heidegger in his accusations of metaphysics. Metaphysics (reflection) and being (contemplation) are orthogonal, but it is important that metaphysical reflection is based on contemplation (rather than delusion). There are contemplative geniuses, who are also masters of conceptualization of that experience (think of Nagarjuna, Dogen or Aquinas) all while knowing that it does not replace the experience itself (or being; ironically, it was Aquinas who re-introduced the concept of being (esse) into the western tradition). There are also great contemplatives who don't do conceptualization (for whatever reason) -- think of masters like Joshu, or John of the Cross if you wish, or a big amount of monks who never wrote anything.

There are also people who have little access to being (no contemplation), yet write papers/books about it -- unaware of their own ignorance. And there are people who are out of touch with being, and don't conceptualize.

The concept of emptiness (just like the concept of being) is pointing at something more than the concept itself, and its understanding comes through contemplative practice (which is called vipassana in buddhism). What I can suggest is that you do a vipassana retreat (I mean, 2 weeks or more), it is really worth it for many reasons, and then you will be able to see better if what they write about Wittgenstein & Nagarjuna and so on makes sense. A good question is what is the use of reading those papers anyway :)

(PS: I am a philosophy major and have later experience with vipassana.)

The term 'misunderstanding' does not has the same meaning for a philosopher and a Buddhist. From the Buddhist perspective misunderstanding something means not seeing with one's own mind, not being able to see empirically. As for most philosophers, understanding only requires the ability to understand language and being able of logical analysis. Metaphysics is mostly subject to speculations about what is 'meta' (after, behind) 'physics' (empirically perceivable nature). I'm sure there are exceptions, i.e. Aristotle is said to be a big empiricist, but in Buddhism there's the big difference that words and terminology are useless.

As for misunderstanding the concept of emptiness, in Buddhism concepts don't really exist because you can't experience them (you can only experience thinking itself, you can't experience 1 + 1 = 2 for example), but emptiness is claimed to be a real experience. That being said, Buddhists would rather speak about the emptiness of concepts, claiming that theoretical knowledge won't bring you any insight. This is probably not a satisfying answer for you particular question, but since this is the Buddhist SE I hope it's good enough...

A suitable quote from Ajahn Chah:

If you don’t practice you won’t know. Frankly speaking, you won’t know the Dhamma by just reading it or studying it. Or if you do know it your knowledge is still defective. For example, this spittoon here. Everybody knows it’s a spittoon but they don’t fully know the spittoon. Why don’t they fully know it? If I called this spittoon a saucepan, what would you say? Suppose that every time I asked for it I said, “Please bring that saucepan over here,” that would confuse you. Why so? Because you don’t fully know the spittoon. If you did there would be no problem. You would simply pick up that object and hand it to me, because actually there isn’t any spittoon. Do you understand? It’s a spit- toon due to convention. This convention is accepted all over the country, so it’s spittoon. But there isn’t any real “spittoon.” If somebody wants to call it a saucepan it can be a saucepan. It can be whatever you call it. This is called “concept.” If we fully know the spittoon, even if somebody calls it a saucepan there’s no problem. Whatever others may call it we are unperturbed because we are not blind to its true nature. This is one who knows Dhamma