To be fair, everyone has different preference and how they interpret things. But it doesn't mean there isn't some common UX principles out there and how majority of people see or read things. People make tools and make compatibility with how people use the tools. A iOS news app can introduce sideway swipe or up-down swipe for users to flip back-and-forth, but the app wouldn't ask the user to draw a circle to signal next page and triangle as previous page. Why? Because swiping up/down, left-right looks more intuitive and simpler, more align with how we work with a physical book.
http://uxmag.com/articles/guiding-principles-for-ux-designer...
http://uxmag.com/articles/the-secret-to-designing-an-intuiti...
http://www.uxbrainstorm.org/user-experience-design-as-applie...
How is "new" more clear than "newest" or "latest"? Are you telling me, from the first sight, that there is no doubt that "new" means "newest submission"? And by looking at "threads" you can tell it means "my latest comments"? Of course not. You said people should explore so you are putting the hard work on users.
This is a simple site. We don't need some confusing nav names like threads and comments when the results don't really agree with the title. What constitutes simple and intuitive? You don't call your sign up page Santa and logout page Buddha.
1. new's actual link is newest, don't save 3 char.
2. threads makes no sense. Threads by convention means a collection of post from BBS. Gmail and Google Group enables thread style which expands to an original post and a series of replies. So calling it threads when it actually means MY COMMENTS is reinventing the word.
3. comments is confusing to me, at least, at first glance means global latest comments.
4. ask, what the hell? ASK HN? Where is show (SHOW HN)? Actually, what the hell is /ask anyway? Doesn't that makes it more like "a url to ask a new question"? How does the filter actually work?
5. jobs, okay fine. I did think of job posts.
6. submit, fine, but it becomes confusing when you look at new.
And stackoverflow. While you are entitled to you opinion, I will argue that stackoverflow isn't so bad.
http://stackoverflow.com/
When it said Questions it means Questions, all the questions. When it said users, it means a list of users. When it said tags, it means a list of tags. Though each link provides a filter, so you can filter questions being newest, being feature questions. Sure you can call Questions "Problems" instead. The point is that when you name something, it should match the result it is going to return as much as possible.
And you are telling me that text does not match with the display result? If I tell you click on users, do you expect to find a cheeseburger? No.
A good UX means users don't need to memorize how he got to page X as much as possible. It means there is some path, which is easy to follow. I don't have to create my own solution: click on profile, click on submission / comments. This is like designing a good url and good RESTful URL. Try to make the url match with what it is intended to do and present.
And finally, I do have the right to claim it is wrong or bad, because I am a user. If you think a user cannot criticize or claim that the interface sucks, then app creators don't need feedback at all. Since you claim to be a mathematician, then I can say that a proof is poorly written and hard to follow when the proof uses some confusing, creative notations when the conventions one are good enough to use in the first place. Why draw a knot when QED is good enough.