I am rarely seeing a "Reply" option in the comments under YouTube videos. It is there for a few upvoted comments, but for 99% the reply button is missing! For example, see the comment section of this video: https://www.youtube.com/watch?v=raLkw3_IIFc. You can only reply to the two top comments:
Here is a nice report of the problem from the last year https://www.youtube.com/watch?v=-MuofdTPhEA. Has there been any solution/workaround found since?