I'm not sure what can be done with empty rooms. I think the reason that they have been left out is because they are mostly pointless.
Disagree here. I guess a completely empty stone room might be pointless, but empty (non-combat/skill challenge) rooms don't have to be pointless at all.
I had the same light bulb go off as the OP when I was looking over N1 Cult of the Reptile God. Here's the thread:
http://www.enworld.org/forum/general-rpg-discussion/244799-old-school-modules-space.html
In a nutshell, there is a large dungeon that ends the module and there was a lot of SPACE (e.g., areas with no 4e type encounters)! And the space was intelligent. Here's some examples,
a) an empty room of mud that was similar to other rooms that had mud and monsters -- keeps you on your toes
b) a storeroom that added details of the inhabitants (e.g., cheap wine with a couple bottles of special wine, weird rations for reptiles)
c) a cavern with undead that were acting as a bilge pump by using buckets to bail water out of the cavern, with no chance they will attack unless provoked. Awesome image! (and forshadows a cleric/creature capable of creating undead)
I was pleasantly surprised at the space between combat encounters within the dungeon, and the fact that the space ADDED a lot to the feel of the place.
I agree with the OP. Let's put the explore/space back in the 4e dungeons, as I think the combat encounter designs have been pretty good in published 4e stuff. Space/empty rooms can be a great part of the DM toolkit to add tension, and give the players interesting details of the inhabitants' life that makes the combat/skill challenges more meaningful.