Well, the basic parts of the site are self-evident, certainly to anyone interested in the hacker community. And the other, more esoteric aspects of the site are 1) in the source and 2) occasionally mentioned in articles.
Not sure I would say that it is a red flag about the site.
I would say it's a red flag about the site. It's certainly not a red flag about the person (why should you have to read through the source to work out how the software works? There isn't even a link to the source from the software beyond using a Google search).
I'd say its fun and a challenge to find things by exploration. In some cases, such as poll posting, they are deliberately left unpublicized to prevent over abuse.
Because they're not very useful if nobody knows what they are or what they do.
I suppose they're kind of cute, in an easter-egg sort of sense. But I really don't see why HN just couldn't have a regular landing page or maybe a sidebar with these links on them, along with maybe a caption or tooltip describing what they're for.
Why all the mystery? It really makes the site much less useful for huge numbers of people to keep this stuff semi-hidden.
Not sure I would say that it is a red flag about the site.