Has the proportions of articles to citations changed?
That's a really fascinating question. I looked at the original Nature article (https://www.nature.com/news/the-top-100-papers-1.16224) - my initial intuition would be that the proportion shouldn't differ to significantly from the earlier one (it will most likely differ to some extent as there is no reason to expect the proportional growth of citations and the growth of papers to correlate), but we would of course need to calculate it.
Wouldn't the best course of action be to use a research database where you can filter by number of accrued citations, set that to display papers with &gt; 1000 citations and then divide the retrieved number with the total number of papers in that database? If you you wish to be consistent with the Nature article, I believe they did their analysis solely on Web of Science. Having that said, I'm not sure they provide these figures out of the box, it looks like Nature got special access to these figures for their article.