There are villages_nether.dat and villages_end.dat files in the map data, positioned at .minecraft/_Map Name_/data. The name suggests they are for storing information about villages in the Nether and the End, although they actually (as far as I know) don’t generate in either dimension, only in the Overworld, for which the villages.dat file is used.
Note: I’m currently playing the demo version since I haven’t bought the premium license.
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The villages files don't store information about the physical structures generated with terrain. It stores information about a village, regardless of if it's a result of natural generation or not. You can manually create villages in the other dimensions.
Aside from the name, the files have the same data, at least if one has entered neither the End nor Nether, nor has encountered any villages.