It's still done the same way. I haven't used Quark 6 for a few years now, but in 8, H&J is in the Edit menu. You will see that there are several H&J sets in the default document (I think there may have just been one in Quark 6), and because H&J is a paragraph attribute, editing one of the existing H&J sets won't affect text that doesn't use that particular set, so it's not as simple as it may have been in the past, but still done the same way.
If all of your text is using the Standard H&J set, you could just edit that and be done, but if you want some text with hyphenation and some without, you're better off editing a new set, and applying it to your text. That will be much easier to do if you have been assigning paragraph styles, as you would only need to edit the style itself. If you are using local formatting, you will have to apply the new H&J set as you go.