If you want a game that is not composed of flat levels connected by teleporters, though, you're largely restricting yourself to 3D games. I can't think of any 2D dungeon crawlers that fit that criteria, Diablo included - if the terrain can't be rendered in three dimensions, it's difficult to construct the dungeon any other way (though it could be faked a bit - the Ultima VIII engine could do quasi-3D, I guess). I'm not saying it can't be done, but I've never seen it.
I'm not sure I've ever played a game that would satisfy all the criteria you've listed, honestly. Ultima Underworld maybe, as has been mentioned, but I haven't played that in a looooong time and can't remember much about it.
At the moment, I can't help but recall Shangri-la in Might and Magic III, a small village located far underground. There's so much rock over your head that just walking around is almost suffocating, but it's just an illusion; it's just a two-dimensional map with no Z coordinate to speak of.

I played about 1 hour of it yesterday, and my answer is: yes.

I second Daggerfall too. The sheer scale of some of those dungeons is just sick.

Daggerfall. By sheer coincidence they also double as the worst dungeons.

Until you run into your first ancient vampire, then it becomes a memory of pure horrificness you'll never be able to scrape away.

Demon Souls on the ps3, nuff said.

Stella Deus: Gates of Eternity for the PS2. You can descend up to 100 floors.
I don't remember quite well, but I think Divine Divinity has some deep catacombs. Also, is a great underrated gem every rpg lover should play.

I can't believe it took me so damn long to think of this!
With the original and this, that 612 levels, not many games will beat that

Since you mentioned Morrowind, I suggest you try Aard Vetooch. That's one deep dungeon, with 100 ever more difficult levels, in varied settings.
Or, if you want even more, you could try the Dwemer Graveyard, which has 1000 levels (I can't comment on it, though, as I never got further than installing it).
Both can be found here.

Try Albion, some dungeons later in the game are really huge (and deep).

A very old game but great dungeon crawl is Dungeon master although not sure if theres any npc but its all dungeon

You can check Kikoskia's Let's Play Stonekeep videos at Youtube to see how the game plays. Just don't watch too far if you don't want to be spoiled. He has also made numerous other let's play videos series for games like Ultima 7, Albion, Lands of Lore 1-3, Doom etc.

I think some of the Nippon Ichi games are deeper than that. If I recall, every item had a 100 level item world in Disgaea. Ridiculously in-depth game. A bit too much grinding for my taste. If you like that though, check them out.
Also, I hate them, but I think Fushigi no Dungeon are deep. See also, Fate (I think there's something like 10k levels). There was also an endless dungeons downloadable content pack for NWN that might be of interest.
Also, there's a whole genre of dungeon crawlers for the PC - EotB, Wizardry, M&M, Stonekeep, Arx Fatalis, etc to name a few. Also there are a number of games with one off 100 floor "bonus" dungeons.

Diablo (the first one)