Names in my language used in publications are inconsistant. Should I worry about it?

It's only part of the solution, but you could look at ORCID, which gives you a unique ID to link together all of your publications etc. regardless of the exact form of your name you use. Use isn't widespread yet, but more and more publishers are starting to adopt it, as are increasing numbers of research institutions (at least in the UK).

Among those names you listed, the only place for concern about confusion is that the second representation (Nguyen VD) is not obviously the same as the the third and fourth (NV Du or Du NV). Now in your question you seem to have a couple of concerns.

1) You're worried about authors' names on your CV (I guess in your list of publications). Here the only likely concern should be for it to be clear which author you are. If you're in a field like math, where author order doesn't matter, you don't even need to list your name, just say "(with ...)" to list your coauthors. Otherwise, it's normal to list names as they appear on the paper. If you want, you can take some liberties by expanding to full names or adding diacritics as long as it is easy to identify the author list on the published paper with that on your CV. If for some reason it is still not clear which author you are (e.g., if other authors have some abbreviated name which might be yours), you can highlight your name on each paper (e.g., with an asterisk or use a different color).

2) For your LORs, it's common that different professors refer to people in different ways. Since these will be LORs for you, there should be no confusion of who they're referring to, as long as it's reasonably related to your name on your application. Also, if you list them as references, enter their names in their preferred format is reasonable, at least if you are writing in free form (e.g., you're not given certain spaces for family name versus given name). The committee will then see that the way you entered their names matches with the way they wrote their own names on their letters.

I don't think this will make a bad impression with anyone. If this were to make a bad impression on someone, then you'd probably not want to work for that person.

In particular in the U.S. (but mostly in all Western countries at least), nowadays, it doesn't matter which name you choose. What matters is that you decide on one name, and stick to it. If you don't, you create unnecessary confusion and, at least until you'd be well-established, a never-ending need to clarify simple things.

If it's not too late, I would consider discussing this with your letter writers, and ask them to kindly all use whichever name you decide on. If it is too late to ask them, but you haven't sent anything out yet, do as the comment suggests and add a few explanatory words to your cover letter. And if you've already sent your application out, I wouldn't worry too much about the name issue.