Anyone else tackle this type of problem - your characters will only likely encounter 50% of your areas, so how do you balance enough detail vs too much?
2. Leaving Room for Expansion:
Haha, I guess there have been a few creative solutions out there - the Greyhawk Construction Company comes to mind, as does 'The Fog' I heard was used in Castle Zagyg.
Both of these are somewhat connected and largely depend on how much ground the PCs can cover in a typical session. Once you've got a feeling for that (and it will vary considerably based on the group dynamics), you can detail out about 2 sessions in every direction (horizontally and vertically). That keeps the amount of prep manageable.
Some of this prep will be "wasted" as the PCs don't head in that direction, but there are a couple of mitigating factors:
(1) The PCs are likely to back-track at some point and explore other paths -- either in an attempt to find another route to wherever they're going or just to see what they missed.
(2) If the dungeon is organic and evolving, you'll find opportunities to draw players into this content. They wiped out the goblin clan but didn't move into the ogre-occupied caverns beyond? Well, the next time they head down this way the ogres may have expanded their territory into the freshly-vacated caverns.
Beyond the "two session limit" just keep some rough notes ("here there are shadow-infused orcs led by a banished dark elf prince"; "here there are mindlflayers worshipping the forgotten god-idol of Juntha'thek"; and so forth).
3. What if they don't descend?:
So what do you do if the party levels up, they realize they only scratched the surface of level 1, and rather than descend to level 2 they decide "No matter how long it takes, let's clear this sucker first!"? Megadungeons aren't meant to be exhaustively mapped and stocked, it ruins the aura of 'it's too big to be known entirely'. And besides, after a certain point the challenges will be downright boring.
You're over-thinking it.
Let me re-phrase the problem you're anticipating: "What if my players take the opportunity to do whatever they want and use it to do whatever they want?"
Congratulations, you're experiencing sandbox play.
If your players are having fun trying to clear all of levle 1, then they're having fun. You might think that the challenges are "downright boring", but clearly they're not boring enough for them to go and do something else.
If you're really going to embrace sandbox play, then you're going to have ditch the
fetishization of balance that got its misbegotten start in 3E and ended up hard-coded into the design of 4E.
Get rid of the notions that encounters are supposed to be "balanced". Get rid of perfectly balanced treasure parcels. Sometimes there are bad choices to be made and sometimes there are hard choices and sometimes there are easy choices. Let the PCs steer their own course.
Now, you may run into a situation where the players believe that they're "supposed" to be clearing the dungeon level. So they'll continue doing it even after they've stopped having fun. What you've got there is a misunderstanding of the style of game you're looking for. And the easiest way to fix that problem isn't to try to mechanically brow-beat them... it's to sit down and say, "Look, if you don't want to do this, then you don't have to do it."