If the contents of a hub (whether creative or non-fiction writing) move me to comment, I do so. I realize, however, that the "Deny" button is there for a reason. As far as I know, none of my comments have been denied, but that doesn't mean it won't happen. I would still feel the same about the hub's content and would still vote the same even if the writer did not allow my comment.
If I'm very passionate about a hub's topic, and my opinion differs extremely from that of the writer, I might refrain from commenting if I were concerned that I could not do so in a completely civil manner. (I have been known to get "riled up" over some issues, and I don't want to precipitate an argument online. Ha!) I've read some hubs where one or two readers were determined to argue their points ad infinitum, and the hub writer eventually had to say (in effect), "Enough! You disagree with me, and that's okay, but continuing to wrangle about it is not proving anything or adding to the discussion." At that point, if the argumentative reader continued in the same vein, I think the writer would be justified in disabling further comments by that person.
The only reasons I would ever deny a comment on one of my own hubs would be if (1) the comment were obscene, (2) the intent was obviously malicious or (3) multiple comments degenerated into the type of argument I described in the previous paragraph. A good discussion about an article--particularly if the topic is controversial--usually attracts "pro" and "con" opinions. The writer may consider it necessary to address "con" feedback in order to defend either content, facts or sources (as I did recently). I think that is preferable to disabling a comment just because it might not agree with the hub's content or the views of the writer.
I don't know if, or how, disabling comments affects one's hub score. I did notice, however, that after replying to a very long (11-point) comment to one of my hubs recently (in a reply that was necessarily long), my total HP score dropped five points the next day! Whether or not my response affected the score, I cannot say. That hub score still remains a mystery to me much of the time!