This is effectively a partial answer. It does not seek to respond to the overarching question of whether or not there is a causal relationship between poor air quality and death. I'm not currently aware of any notable sources who have claimed that it does not. It only seeks to address the direct claim that Stan Young's paper "debunked" the existing scientific work the EPA had used to determine it. The answer to that is... not really. He's at best pointed out an indicator of potential concern that should be checked further.
This paper is probably technically correct in its assertions. It assumes bad faith on the part of fellow researchers (effectively claiming that they first acquire their data sets and then poke through them in order to find a particularly juicy conclusion, without including that in their calculations of statistical significance). It was not able to find publication for over a year. When it was published, it was published in a journal with a probable pro-corporate bias. This paper may well be making a valid point about statistical rigor, but "debunked" is a rather severe overstatement for the strength of the conclusions that can actually be reasonably drawn.
The Daily Caller is a Conservative News and Opinion site, reporting on politically charged science news. "Science News" of all sorts is chronically bad at actually knowing what papers are talking about, and "News and Opinion" sites tend to be a little more fast and loose than most, when reporting things that support their ideological position. This finding supports the conservative position. This does not inherently undermine the findings of the paper in and of itself, but it does mean that the article itself doesn't add much (if any) credibility. If you include the tendency towards both sensationalism and inaccuracy of science news in general, it means that the claims that initiate in the article may require particular scrutiny.
Regulatory Toxicology and Pharmacology is a monthly peer-reviewed scientific journal. The editor is Gio B. Gori. Wikipedia suggests that he's spend the past few decades working more or less directly for cigarette companies, and googling his name seems to support that. The journal is published by the International Society of Regulatory Toxicology and Pharmacology (http://www.isrtp.org/) which openly acknowledges that they have as one of their major objectives "identifying and engaging the policy makers and scientists who would be most concerned with developing, modifying, or applying those regulations, or affected by their development, modification, or application." - or, in short, lobbying. The Journal clearly describes itself as being intended to support policy decisions. Wikipedia suggests that the institute is financed in part by the tobacco, pharmaceutical, and chemical industries. Their own webpage merely states "Sponsors to be announced soon", and looks like it has done so for multiple years. None of this is proof of anything, but the most likely state of affairs given the available evidence is that the institute is largely a pro-corporate lobbying group that does not wish to make that obvious on their website. That in turn would imply rather heavily that the journal would be at least somewhat biased. It is peer-reviewed, and these conclusions are not nearly enough to suggest that it will knowingly publish things that are false or lack academic rigor, but there is a good chance that the choice of which papers to consider may be influenced by political slant.
The paper, on direct observation of the abstract https://www.sciencedirect.com/science/article/pii/S0273230017300673, appears to be selecting eight papers that were used in meta-analysis papers, looking at the available information, determining how many things could have been tested for with the given data, and then asserting that random chance would have produced a reasonable number of apparently statistically significant results, and thus that the meta-analysis results aren't as compelling as they might be. It was also mentioned (in the Daily Caller) that he had to shop it around for a few years before he got anyone to publish the thing - suggesting that no one was willing to publish it until he got to the industry-friendly ears at Regulatory Toxicology and Pharmacology.
So, short answer is that it looks like the paper is probably technically correct, and it may even have a valid point (saying that people are acting with more certainty than they really ought to have without a few more tests), but it's not anything like as strong as "debunked".
To clarify further, at least by my understanding of Young's abstract, he's essentially assuming bad faith on the part of the researchers of the papers he is studying. His thesis appears to be, in essence, there are enough possible questions that could be asked of the datasets in question that someone who was willing to take their time to pick and choose could easily find questions that would appear to be statistically significant, even if the input data was noise. He concludes from that that the papers in question, and all meta-analysis papers based off of them, are unreliable. It is not clear from the abstract how how chose his eight example papers, given that there are apparently over 100 papers on air quality available.