Despite 1.6.4 saving structure data in the world to prepare for 1.7, Witch Huts don't seem to be included.
When I loaded up a world with a witch hut in it in 1.6.4, there was no witchhut.dat when I looked inside the save folder. I saw Mineshaft.dat, Village.dat and Stronghold.dat, but no Witchhut.dat. I expected to see the Witch Hut saved in the data.
How to reproduce:
Start a new world with the seed '2' (Yes, just the number 2). There is a witch hut at x: 3 z:160. Close Minecraft.
Then go into your Minecraft saves folder at %appdata%/.minecraft/saves. Click on the world you just created, then click on the 'data' folder. Inside you should find names of structures, but no witch hut file.
Witch huts are saved in the Temple.dat.