These threads long predate Bonsai: https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que.... So does the practice of linking to related YC startups from 'official' HN pages. For example, the Feb/March Who Is Hiring pages had links to Manara at the top (https://news.ycombinator.com/item?id=26304051), and https://news.ycombinator.com/jobs has had many links to YC startups doing recruiting-type things over the years (Triplebyte, KeyValues, and many others). The Bonsai thing is just another example, though I suppose it's been up there for quite a while now.

There have been many other cases not related to recruiting. HN Search is an example, since it started as a link to Octopart (YC W07) and now points to Algolia (YC W14). I remember other one-off things like an OAuth-related startup and a carbon-credit startup which used to be linked from the HN footer.

Eventually we change the links.