I could be wrong, but I think the karma threshold for endorsing has been lowered. I'm at ~850 and I'm able to endorse comments.
I feel bad that comments posted just to say they agree with someone/something cannot/will not be seen. This type of 'noise', as long as it is sprinkled lightly throughout, isn't so bad, in my opinion. I mean, I understand HN is meant to reward thoughtful comments, but at what point does this concept go into Less Wrong-type of ridiculousness? I'm totally not trolling, but we're only human. To deconstruct all aspects of a community/forum to only allow strict logical/cerebral behaviour seems like a community I would rather not be a part of.
In the end, I'll probably not endorse any comments, or at least extremely little, because I don't know if I agree with the concept and would rather not get involved.
I'm probably in the minority here, though.
Unfortunately, most of my comments of this nature are replies to unpopular comments. I feel no need to tell someone I like their work if everyone else is already doing the same. However, this system may make comments designed to be read by only one other person a thing of the past.
If you have something to say, even something fairly light, I expect it will still get unpended.