I think part of the problem is that dungeon levels are part of the game's in-built difficulty "switch". The whole system is built around an assumption that levels are going to be largely independent of each other, and will increase in difficulty as they go deeper. If you plonk a big room somewhere that plunges through multiple levels, then the players can get (literally) beyond their depth much more easily than normal.I agree. Players are supposed to be able to roughly gauge their risk based upon the level they're on. But I also think it's important to yank that rug out from under them every once in a while. And sometimes the party's intelligence about the WMDs is just going to be plane wrong, owing to stairs that don't really change the level you're on or mistaking stairs up to level 3b for a route to the main level 3 or rooms that sink imperceptably or all sorts of stuff like that.
Not that such a situation would necessarily be a bad thing, of course, but I do wonder how many designers are reluctant to do so because they're unconsciously obeying these in-built principles of "game balance".
And here's a comment from Restless:
A novice DM should entirely ignore my suggestion. Feel free to consider my ideas about 3D dungeons as an advanced technique that's probably more suitable after you have a couple Easy Stack™ dungeons under your belt. I'm not saying a newbie would be incapable of doing a good 3D dungeon, I'm just opposed to anything that makes getting over that first time DM hump any harder.
This [my proposal for planning 3D spaces] runs a bit counter to the notion that you may build a megadungeon organically by just putting together three levels and getting some players in there to start mixing things up. To do this sort of thing properly requires planning that might squelch some ideas or lock you into others.