Will monsters spawn in a Minecraft dungeon if you flood the floor?
The rules for "normal" spawns do not seem to apply fully to Mob Spawners. A dungeon with a completely flooded floor is not safe. Apparently the random block in the 9x9x9 cube can be air.
Here's a flooded dungeon, and here's the same dungeon after I turned the difficulty to Easy (and removed the torch). The spider spawned in the water and climbed up to the ceiling.
Edit: Test repeated with source blocks, and a torch for better visibility.
Setup
Result: still not safe
A Mob Spawner can definitely still spawn with a room covered in water. I have created a skeleton trap with completely water covered floor to sweep the skeletons down into a pit to drown, as well as sweeping the items out to me.
Mobs can't spawn in water, even from Monster Spawners! The special rule of spawners is that they can spawn mobs in midair; their spawns still require appropriate (lack of) lighting and an empty space, but they do not require an opaque block underneath like normal monster spawns do.
It may appear that mobs are spawning in water since they immediately fall in, but if you were to completely flood the room (no air blocks anywhere in the volume, only water blocks), no mobs would spawn.
For purposes of creating traps, this means the most efficient design is to make sure the 8 × 3 × 8 space around the spawner (and one more layer upward if spawning tall mobs, i.e. skeletons or zombies, and one more block sideways if spawning spiders) is empty air, and place water two blocks (or lower) below the spawner to carry mobs away.
I have reviewed the current version of the Monster Spawner page's Spawning Behavior section at Minecraft Wiki, and it appears to have its facts correct; it covers what I have mentioned here and more.