As far as the company posting the listing is concerned, the bad outcomes are (a) if the candidate they would otherwise hire won't apply because of the content of the attached discussion, and (b) if candidates that they aren't interested in hiring apply because of the attached discussion.
I think, since HN seems to exist mostly for discussions about how awful open office plans are, and since many of the company posting listings have open office plans, then the discussion will usually be negative, but that seems more likely to cause the opposite of (b) (that is, less unwanted candidates) than it will cause (a), since people who are 'a good fit' for the job would be less likely to be dissuaded by the sort of baseline negativity that exists in most of the comment sections on this site than people who aren't qualified or aren't interested in working for that company specifically.
I always suspected it was to prevent people from talking about embarrassing things about the company. People are very good finding faults and even making innocent things look evil. Easier to avoid all that by simply disabling comments.