I generated a new world using the snapshot and spotted a structure generated underwater. It turned out to be the portal room of a stronghold - see screenshot (seed and co-ords included).
There was no sign of any other stronghold structure anywhere nearby and the portal room was "floating" some distance above the ocean floor. This was in one of the new Deep Ocean biomes.
Not sure if this is a bug or just a quirk of this particular seed but thought you would want to check it out.
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Confirmed.
I regenerated this world using 13w36b and the stronghold portal room was still in the same place. However, on further investigation, the rest of the stronghold is there, inside the two island in the background of my screenshot, it just isn't connected to the portal room.
I found this in a deep ocean as well. Newly generated world in 13w38c. Seed: 1100924296 at 946x , 55y , 357z. I didn't check around much, but there definitely are not any nearby large vertical islands like those.
Confirmed for 1.7.4, 1.7.5 and 08a
I have seen this as well, but the rest of the stronghold was there, but under the seafloor (in the ground).
Tested just now on my server seed (-368165910821204477) running Minecraft 14w32d and the Stronghold at X=496, Z=816 still generates with the portal room above the ocean floor. The rest of the structure seems to be in bits and pieces underground, with none of the corridors connecting with one another. Still needs fixing!
Why is this marked as WAI?

Why is this marked as WAI?
Because it is working as intended. Mojang doesn't have to justify why they did something.
Even though it was marked "Works as Intended," it was still "fixed" in 1.13. This was caused by the game not generating parts of the stronghold if they would be too close to water, with the exception of the portal room. This could also isolate other parts of the stronghold. 1.13 removed those restrictions on stronghold generation. Even though 1.17 made it so that underwater strongholds are buried below the seabed, the water still does not isolate any rooms.
It wouldv'e been cool if the entire strong hold was generated... new underwater temples sounds epic... would need the new water breathing potions to complete to so I wouldn't put it past mojang