I would in general agree with you, but having read through the journal paper: I think the fraction of general audience newspaper readers who could actually read that paper is very low. I come from a science background, spent time dabbling in time and frequency measurement enough to understand some of the concepts, and still found it a painful slog. (I am very much not a physicist!)

I still think it's the right practice for newspapers to always link to the primary source, but in this particular case I understand why they might make an editorial decision not to.

Is there evidence that is the actual reasoning, because I find it ridiculous. People who don’t care about the primary source are not going to follow a link to, e.g., a court ruling, government report, fed minutes, a leaked document, a research paper, etc; but those who are interested are going to immediately leave the site and likely not come back for a long while.

Am I missing something?

This is actually very rare for the New York Times - they're the only major publication that regularly links to the original sources.