As if there weren’t enough problems associated with including doors and secrets in a dungeon — once the primary threat of a dungeon has been eliminated, the players can plumb its depths with impunity. Once the danger’s gone, where’s the fun? The immediate problem is when finding secrets becomes “too easy.”
How do you maintain an appropriate level of tension when the players have disabled the biggest bad in a dungeon? The first idea that came to mind was to have some time-sensitive, external mission or objective riding on the party’s completion of the crawl. They entered the dungeon for a reason.
Wandering monsters could also play a role in maintaining tension in the dungeon once the “big bad” has been dealt with — there’s a concept of a “power vacuum” when a dungeon has had all its occupants slain — especially its leader.
This would be the monster-swarm equivalent of a Load-Bearing Boss. The party must quickly escape the dungeon before whatever the boss was holding back comes looking for blood — the party’s blood — or anyone’s, really.
Looking briefly at the “dungeon scores” I’m developing for the rapid creation of dungeons, is the score that’s given me the most trouble lately… “Resources,” or “Materials,” or more recently, “Auxiliary.” The basic idea is that even a dungeon doesn’t exist in a vacuum — except when it becomes a power vacuum?
…From an ability score perspective, Auxiliary is rolled whenever there’s a chance for a wandering monster encounter, or reinforcements arrive to help defend the dungeon from invaders (the adventuring party). It’s largely unimportant who the reinforcements are — they might be opportunists arriving head of the pack.
Getting back to costs though — time has to be a factor for many of these solutions to work. And there has to be some consequence associated with spending time, however fruitful it proves to be. On occasion however, the PCs might be allowed to take as much time to search a dungeon as they like. But only rarely.
As suggested above, without any risk — where’s the fun?
Make sure the players know ahead of time if there’s a time limit on searching the dungeon. There are plenty of things to hang over their heads while searching before the dungeon’s been “cleared” — if they defeat lots of minions but save the “boss” for last — he could always come “searching” for the party.