I've always suspected it's an attempt to defuse flame wars, with the expectation that a lot of comments means a post is highly controversial and stirring up arguments in the comments section.
Seems unlikely. Using comment count as an indicator of poor quality discussion would treat topics with intense interest and engaging discussion like flame wars.
So, I find this explanation hard to believe, especially given that the mods here are active, and that there are other mechanisms for exposing flame wars (including flagging, down votes, etc).
High-quality posts will usually be upvoted by lurkers, ensuring a favorable upvotes-to-comments ratio. But yes, it's a blunt instrument that sometimes has false positives where the mods intervene to turn off the penalty: https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...