Paid submissions are already disclosed by the inability to vote or leave comments. They also tend to be by one of a few companies looking for developers.
Both of those aspects keep the ads in check.
Based on how the (down)votes go, I would give it a fair chance to the HN crowd turning into a "general interest" one.
The question stands: should cross promotion deals be disclosed?
I've noticed that for a lot longer, and for a lot more than just the New York Times.
> either the HN crowd is turning into a general interest one
The thing about "general interests" is that they are often shared even among members of a community centered around more specific special interests.