One good reason, demonstrated almost everywhere that hashtags exist, is that once you have them, it becomes trendy to play games with them involving dishonest tagging or jumping on a popular tag with no meaningful contribution (often both together).
Hashtags are also visual noise, though that's probably easy to manage, e.g., by allowing hashtags as part of the text entry, but then treating them as tags but not displayed parts of the comment text.
Comments here seem to assume that hashtags would have to be implemented exactly as they are on Twitter, where anyone can tag their comments with any tags, which wind up appended to the text of the comment itself.
Obviously, that wouldn't work with HN's culture, but those are implementation details, not requirements. And as far as search goes, the purpose of hashtags (when used properly) is to basically make searches more efficient by providing a set of common keywords directly related to the context of a comment.
Hashtags could be added to Hacker News without much disruption - lobste.rs uses them and I don't think anyone would accuse that site of having descended into lulzy random chaos as a result of them. It's just a matter of having the implementation fit the culture.
The ability to add tags, like the ability to flag or vouch, could be conditional, based on karma and revocable if abused. Tags could begin in a hidden state similar to dead comments, needing to be vouched by the community and to pass a certain threshold of votes to become visible. Tags could only apply to threads (not comments) and could be limited to, perhaps two tags for a thread.
Also, tags could be hidden by the user if desired (this should probably be the default.)
It is possible to enhance user experience without degrading the quality of the site, or being intrusive. The list of new features people assumed would destroy HN, but haven't, includes thread folding, show HN, mobile styles, vouching for dead comments, and even fixing a bug that would cause comment links not to work after a few minutes.
Comments are made of words, which one can search for. How is "#this #text #more #searchable"? Less readable, that's for sure. I never understood why one would use hashtags, except as a joke. #lol #wedontneednohashtagz
Aside from what was mentioned, hashtags are not standard. You'll get people using "#javascript", "#js, "#nodejs", and "#node". Standardizing tags is possible but requires a lot of moderation time or a small community. Lobsters[1] has a good tag feature, for example.
I personally had read an article and want to go back to it couldn't find it. Also, I don't really like reading about of a lot of stuff I would like to filter out.
Hashtags are also visual noise, though that's probably easy to manage, e.g., by allowing hashtags as part of the text entry, but then treating them as tags but not displayed parts of the comment text.