If FFXI is anything to go by, then it's safe to say that SE wants diversity. That's what really set FFXI apart from other mmo's I've seen, it had a lot of different things to do, especially at endgame.
So my bet is that yes, some NM's will drop gear, others will drop mats for gear, others still will probably drop something else completely, and some will likely have junk drops or even quest items.
Just like at endgame, there will probably be open area HNM's, as well as instanced/leve HNM's much the way FFXI had KSNM HNM's. There will probably also be a number of different endgame sections, at least one of which will be similar to "raids".
The real nice thing about SE is that they don't pick one thing, such as raids, and make half a dozen of them, and call it endgame. That alone is enough to make me like SE's mmo's more than any other, but they have plenty of other stuff going for them too. Crafting is one of those things, and will ALWAYS be a crucial aspect of the game, whether you craft or not, it will still play a big role in your characters development. No, you can't powerlevel it in a couple days... But you're not supposed to. Some will craft a little for things like repairs, others will master the crafts, and buy the craft mats that drop off rare mobs, i.e. the new scorpion claws and behemoth hides. Some will ignore crafts entirely, and supply the consumer aspect of the economy for the crafters.
NM's will also always have a place. They are adding them to open areas for those who like the competition of camping and the thrill of the hunt, because though many don't get a kick out of it, there is definitely a thrill to getting the claim on a rare NM. For the others, they will be appearing in leves, though the details remain undisclosed. That at least insures that you won't have to worry about others poaching the claim, but will still be able to experience the fights.
Really, anyone who played FFXI I think should know what to expect from this game. Yes SE is moving in new directions here and there, but it is obvious that they did not become a whole new team overnight, and there are clear similarities. They cater to a diverse yet niche crowd, but they do so very well, the rough launch excluded.