The other way to look at it - 97% didn't react to your shameless plug, and probably a good chunk of these were annoyed by it. An ad is an ad, regardless of how you call it.
On the other hand, 99.7% of my readers didn't react to my website in the first attempt, so it is a net positive anyway. And, from a marketing point of view, those who are annoyed by that most likely aren't going to hire you anyway.
The author could start to answer the annoyance question by AB testing the plug and looking at reengagement figures and time spent of the two segments. No drop off in time spent or second visits would be a pretty good indication there's no significant annoyance. I think this can be done quite easily with Google Analytics and his AB test library.
Its not so black and white, a pop up is way more annoying that some text at the end of the article. And what is more relevant, the user just have to stop reading and just close the page, two actions that the user was going to eventually do even if there was no ad; but pop-Ups and video ads make the user lose resources (time) and it requires a special action to be cancelled (look up for the little ex in the corner and click it). Also because is text and not and imagen it does not significantly distract the user from reading the article. Also the fact that is highly relevant (consulting for companies/startups and a scrip to improve HN reading) makes it more acceptable.
In this order of ideas related shameless plugs are better than most other forms of advertising.
I think that's a pretty bold claim. I can't remember ever being annoyed by a blog post which included a brief "This is me and what I do" plug.