The question about comment points is "do I think HN works better if comment points are hidden for all users", not "do I want to see comment points myself".
And to the second point, HN is PG's experiment with the programming language he's developing and the community for his company more than an example of modern web design. The point is probably that tables were quicker and easier.
Rendering a page as a semantically structured document won't remove the ability to globally disable a feature. (In fact, I would argue that it would make it easier.)
It's fair enough that pg does whatever he likes... no one can argue that point.
And to the second point, HN is PG's experiment with the programming language he's developing and the community for his company more than an example of modern web design. The point is probably that tables were quicker and easier.