I hate to say this, but if you actually have to ask the developer for some simple docs on something basic like this, that's a big red flag to me.

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.

why is it a red flag?

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.

It's posts you've upvoted.